Grays Harbor Juvenile Fish Use Assessment: 2013 Annual Report

Transcription

1 Grays Harbor Juvenile Fish Use Assessment: 2013 Annual Report Prepared for the Chehalis Basin Habitat Work Group and the Washington State Recreation and Conservation Office August, 2014 Prepared by: Todd Sandell, James Fletcher, Andrew McAninch and Micah Wait

2 Sunrise at Stearn s Bluff, South Channel, 2014 Tidal Marsh near the mouth of the Humptulips River, 2014

3 Table of Contents Index of Figures... 1 Index of Tables... 2 Executive Summary... 3 Section 1: Introduction Purpose and Objectives Study Area...9 Section 2: Methods Habitat Inventory/ Sample Site Selection Habitat Area by Salinity Zones Field Sampling Methodology Age Class Assignments Catch Calculations/ Fish Densities Section 3: Salmonid Results Salmon Growth/Age Class Salmonid Catch Totals (Raw data) Salmon Distribution and Timing (Densities) Chinook salmon Coho salmon Chum salmon Coded Wire Tag (CWT) Recoveries/ Genetic Analysis Section 4: Non-Salmonid Species Non-Salmon Species Catch Summary Annual and seasonal composition of the estuarine fish community, Non-Salmonid Species Abundance: Baitfish and Unusual Catches Section 5: Fish Community Modeling : Site Modeling Physical Variables : Salmon Abundance and Occurrence Modeling Chinook salmon models Coho salmon models Chum salmon models... 60

4 5.3: Escapement estimates for Grays Harbor salmon Section 6: Synthesis and Recovery Priorities Salmonid Spatial and Temporal Habitat Usage Chinook Salmon Coho Salmon Chum Salmon Trout Analysis of estuarine modifications (for restoration) Acknowledgements References Appendices Appendix 1: Core and secondary sites sampled, Appendix 2: Salmon density by habitat type, Appendix 3: Juvenile Salmon Density and Distribution Plots, Appendix 4: Juvenile Dungeness Crab Density and Distribution Plots, Appendix 5: Online resources for estimating tidal heights Appendix 6: Stream flow on the Chehalis River at Porter, WA, Appendix 7: Juvenile Salmon FL Scatterplots by Species, Appendix 8: Juvenile Chinook salmon hatchery vs. wild FL growth curves,

5 Index of Figures Figure 1: Location of Grays Harbor (the Chehalis River estuary) in Washington State, U.S.A Figure 2: A map of the Chehalis River estuary (Grays Harbor), showing the six zones and locations of the core and secondary sites sampled Figure 3: A map of the Chehalis River estuary showing the six zones and the distribution of the habitat classification types Figure 4: Box plot showing the range of surface salinity at the sampling sites, Figure 5: Map of Grays Harbor showing the salinity zones used to calculate habitat areas in Section Figure 6: Chinook salmon (YOY) fork lengths (mm), by month Figure 7: Mean fork lengths (FL) of hatchery and unmarked YOY Chinook salmon compared by year Figure 8: Coho salmon fork lengths (mm), by month, showing age class designations Figure 9: Mean fork lengths (FL) of yearling hatchery and unmarked coho salmon compared by year Figure 10: Chum salmon fork lengths (mm), by month (all chum salmon are YOY) Figure 11: Mean fork lengths (FL) of chum salmon (all are YOY) compared between years; asterisk Figure 12: Chum salmon catch by month in Grays Harbor, (*February sampling only occurred in 2012) Figure 13: Chinook salmon catch by month in Grays Harbor, Figure 14: YOY Coho salmon catch by month in Grays Harbor, Figure 15: Yearling coho salmon catch by month in Grays Harbor, Figure 16: Monthly catch of salmonids by % salmon species composition, Figure 17: Density and distribution of unmarked YOY Chinook salmon, Figure 18: Density and distribution of hatchery YOY Chinook salmon, 2013 (starting with first month of capture; empty panels equal low/zero catches) Figure 19: Density and distribution of YOY coho salmon, Figure 20: Density and distribution of unmarked, yearling coho salmon, Figure 21: Density and distribution of hatchery, yearling coho salmon, Figure 22: Density and distribution of chum salmon (all YOY), Figure 23: Genetic assignments, by population and evolutionarily significant units (ESU), of Chinook salmon sampled in the Grays Harbor estuary, Figure 24: Common non-salmonid species shown as percentage of non-salmon catch Figure 25: Bar plot showing the three year totals of the most abundant fish species caught in the Grays Harbor estuary, Figure 26: Annual composition (%) of the eight most abundant fishes, Figure 27: Seasonal composition (%) of salmon and the most abundant non-salmonids, Figure 28: Seasonal composition (%) of the seven most abundant non-salmonids, Figure 29: Plot of the Principle Components Analysis (PCA) with three variables Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 1

6 Figure 30: Annual escapement estimates for salmon in Grays Harbor from Figure 31: Map showing habitat alterations in Grays Harbor, by modification type Figure 32: Chenois Creek area habitat alterations, North Bay Index of Tables Table 1: Summary of Grays Harbor intertidal habitat types by zone (in hectares) Table 2: Total area (in hectares) of each habitat type within each salinity zone Table 3: Percent of total area of each habitat in each salinity zone Table 4: Mean annual densities (equivalent to CPUE) of Chinook, Chum, and Coho salmon for Table 5: Chinook and coho salmon fork length (FL) age class cutoffs (mm) Table 6: Annual salmonid catch totals for , by species and origin Table 7: Total non-salmonid catch by species for , in order of annual abundance Table 8: Results of the Principal Components Analysis (PCA), combined ( TideStag =current direction, TideHt =tide height, and WaterTem=temperature C) Table 9: Variables used in GLM models used to predict salmon occurrence across space and time in the Grays Harbor estuary Table 10: Model selection results for GLM models relating Chinook salmon abundance and occurrence to time of year, and environmental variables Table 11: Model selection results for GLM models relating coho salmon occurrence and abundance to time of year, and environmental variables Table 12: Model selection results for GLM models relating chum salmon occurrence and abundance to time of year, and environmental variables Table 13: Escapement values defining the interquartile range, or normal productivity year, for fall Chinook, coho and chum salmon Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 2

7 Executive Summary Grays Harbor (the Chehalis River estuary) is the second largest estuary in the state of Washington, covering 23,504 hectares 2,350 km 2 (23,504 hectares) at mean high highwater from the mouth at Westport to Montesano, and encompassing the tidallyinfluenced lower reaches of the Chehalis, Humptulips, Hoquiam, Wishkah, Johns and Elk Rivers as well as several smaller tributaries and sloughs. The total drainage area, including all of the above tributaries, is 6,605 km 2 (660,450 hectares), with 79% of the fresh water input from the Chehalis River. Within the Chehalis basin there are numerous distinct stocks of native salmonids that are important to the overall biological diversity in Washington State. These include one stock of spring Chinook salmon (Oncorhynchus tshawytscha), one stock of summer Chinook, seven stocks of fall Chinook, seven stocks of coho salmon (O. kisutch,) two stocks of fall chum salmon (O. keta), two stocks of summer steelhead trout (O. mykiss), and eight stocks of winter steelhead (WDFW and WWTIT 1994). In addition, cutthroat trout (O. clarki) have been observed throughout the drainage, and bull trout (Salvelinus confluentus) have been documented as present, but specific distribution data do not exist. All of these stocks have been in decline, as have most salmonid stocks in the Pacific Northwest. The objectives of this project were to develop a scientific basis for the evaluation of potential sites for future habitat restoration and protection projects (as well as identifying construction windows for those projects), to determine the seasonal trends in estuary residence, and to identify potential fish health issues resulting from external macro-parasitic infections. The specific goals were to document the species composition, distribution, relative abundance, habitat use, and timing of juvenile salmonids and other fishes in the Grays Harbor estuary, from riverine tidal waters through marine habitats. The majority of the sampling was conducted using fine meshed beach seines which were deployed at 25 sites using a motorized skiff or set by hand. In 2013, sampling began during the first daylight low tide series in March and continued through mid-september; we made a total of 574 beach seine net sets. Though this project focused on juvenile salmonids, abundance data on all other fish species caught were also recorded had the highest salmon catch of the three years, with 25,792 salmonids captured, even though sampling effort was roughly equivalent to that of 2012 (see below for CPUE data), and slightly fewer seine sets were made than in While this study focused on salmonids, it is important to remember that they make up only a portion of the estuarine fish community (23% of the total fish catch in 2013). As in previous years, chum salmon dominated the catch; 18,633 were caught in 2013, a substantial (15%) increase from 2012 (comparison with the 2011 chum catch is not possible due to a later Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 3

8 start to the sampling season in 2011; see Tables 4, 6). The next highest catch (N=5,706) was of unmarked (mostly young of the year, YOY) Chinook salmon, nearly 17% fewer than in 2012 but 24% more than in There were 504 marked (mostly adipose clipped) Chinook captured in 2013, a 9% increase from 2012 and an 21% increase over Coho salmon were less abundant but still fluctuated considerably; 810 unmarked fish were caught, a 14% increase from 2012 but roughly 40% less than the 2011 catch (the majority of these were YOY). The catch of marked coho salmon (mostly adipose fin clipped yearlings) continued a downward trend, declining 66.3% from 2012 and 74% from the 2011 total. In addition, 15 steelhead, 85 cutthroat and 6 rainbow trout were captured in 2013; no bull trout or sockeye salmon were captured in 2013 (Table 6). Chinook Salmon Overall, juvenile unmarked Chinook salmon catch was lower in 2013 (N= 5,706) than 2012 (N= 6,876) and higher than 2011 (N= 4,322). Catch per unit effort (CPUE) for each year was as follows: 118 fish/ha (2011), 201 fish/ha (2012) and 141 fish/ha (2013). Chinook salmon were the second most abundant salmonid captured (after chum salmon) and were present during all sampling months in all three years. Very few yearling Chinook salmon were caught throughout the study, a result that closely resembles that of an earlier study in the Chehalis basin (Deschamps et al. 1970). The temporal patterns of abundance varied between years: in 2013 Chinook abundance peaked in April before steadily declining through the rest of the season; in 2012 abundance increased through May then steadily declined throughout the rest of the season; and in 2011 Chinook abundance dropped unexpectedly in June before bouncing back in July, then decreasing through September. Hatchery YOY Chinook were present in the estuary mainly from June through August (though present in May and September), slightly later than in 2011, when they were present from May through September. Unmarked YOY Chinook salmon where widely dispersed throughout the estuary during late spring and early summer and showed a clear seaward migration pattern as the sampling season progressed. However, the regression modeling shows that although abundance decreased later in the year, occurrence did not YOY Chinook salmon continued to utilize estuarine habitats into the fall. Unmarked YOY Chinook salmon steadily increased in fork length from February through September. They were notably less common at intertidal pebble, gravel and sand habitats, and both their presence and abundance were negatively correlated with temperature. Hatchery Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 4

9 releases of fall Chinook salmon took place in May and June during the period of this study, which agrees with the observed peak occurrence in the main estuary. YOY hatchery Chinook occurrence was higher in several habitat types including intertidal mixed fines, intertidal mixed fines/seasonal aquatic vegetation, and intertidal pebble/gravel/sand; all intertidal habitats which occur in the main estuary. Coho Salmon Juvenile unmarked coho salmon catch was slightly higher in 2013 (N= 810) than 2012 (N= 694) but much lower than 2011 (N= 1,370). The capture of yearling hatchery coho in 2013 (N= 33) was much lower than previous years (N= 129 & 98, in 2011 & 2012 respectively). Unmarked YOY coho were present throughout the sampling season, though at very low abundance in March and September; marked coho were only present March, April and May. The abundance of unmarked coho peaked in June of 2013, and the YOY were caught mainly in the inner estuary in all months, particularly in the Hoquiam River system. Yearling coho, though present at lower densities, were more dispersed through the central estuary, South Bay, and North Bay, with a pattern of input from the Humptulips River from March-June. The mean fork length of YOY coho salmon steadily increased during the study from April to September; there was little increase in mean fork length from February to April. Coho salmon occurrence and abundance was negatively correlated with salinity; when salinity exceeded 5ppt their occurrence declined quickly, and above 20ppt they were essentially absent. Occurrence of unmarked YOY coho was greater in mixed fines or mud channel/forested sites and backshore marsh/forested sites, habitats which are associated with lower salinities. This suggests that YOY coho are rearing in the estuary for extended periods of time, unlike the yearlings, which quickly migrate to sea. Chum Salmon More juvenile chum salmon (all are YOY) were captured in 2013 (18,633 than either of the previous years, although sampling began later in Chum salmon were present from March to May, with very few present in June. Mean fork length increased throughout the months they were captured in Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 5

10 As with the other species of juvenile salmon, the mean fork length of juvenile chum gradually increased from March (approximately 42 mm) through May (approximately 50 mm). The overall catch of chum salmon was higher in 2013, so a possible explanation is that the higher abundance of chum salmon in the estuary may have resulted in more competition, encouraging the chum to move to sea earlier. The mean FL of chum salmon captured in 2011 was also significantly lower (p<0.001) in 2013 in comparison with both 2011 and Chum were widespread throughout the estuary in March and April, and by May they were at much lower densities in the surge plain as the fish pushed through to the estuary. Peak abundance occurred in March in 2013 (compared to April in 2012). The regression models for chum salmon indicate that timing was the most important factor explaining abundance and occurrence in the estuary. In addition to timing, abundance was positively correlated with intertidal habitats which are most common in the main estuary: intertidal mixed fines, intertidal mixed fines/seasonal aquatic vegetation, and intertidal pebble/gravel/sand. Trout Only 15 steelhead trout were captured in The 2012 catch was far higher (N=85), but the majority of those were captured in one set most likely (based on nearly identical FL) consisted of a single hatchery release group (N=68 hatchery, 13 unmarked). In 2011, 24 steelhead were captured; overall, the low catch numbers preclude any comparison of their habitat preferences. Slightly more cutthroat trout were caught in 2013 (N=85) than in 2012 (N=65), although the peak catch was in 2011 (N=92). Though cutthroat trout were encountered infrequently, enough were captured over time to observe some patterns of estuary use. Cutthroat densities were highest at scrub/shrub cover and emergent marsh sites, although some were also caught in every habitat except cobble/gravel/sand beaches and sand flats. Their densities closely aligned in space and time with those of YOY Chinook salmon, suggesting possible predation. Our catches of cutthroat trout demonstrate that this species is present in Grays Harbor through much of the year (March to September), though they were most commonly encountered from April to June. No bull trout were captured in 2013; previously, seven had been captured (3 in 2011, 4 in 2012) and sampled for genetics before being released. All of the bull trout were captured between March and early June, when water temperatures were low. While they may have remained in the estuary beyond June in deeper, tidally cooled channels, they avoided shallow channel margins and tributaries Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 6

11 where we may have encountered them via beach seining. All of the bull trout were captured in the Johns River (2), lower Hoquiam River (1), Inner estuary (2) or South bay (2) zones. Coded Wire Tags (CWT) and Genetic Analysis: Two yearling coho (one wild and one hatchery origin) and a subyearling Chinook salmon were recovered with CWT in The Chinook salmon was released from the WDFW Forks Creek hatchery in Willapa Bay, the wild coho salmon was tagged in the upper Chehalis River (near RM 52) by the WDFW Wild Salmon Production Evaluation unit, and the hatchery origin coho was released from WDFW Bingham Creek hatchery on the East Fork of the Satsop River. Results from the fin clips collected for genetics in 2012 and analyzed by the WDFW became available in June of These were collected to test the hypothesis that juvenile Chinook salmon from outside the Chehalis Basin utilize the Grays Harbor estuary for rearing (because so few CWT fish have been recovered). Note that not all juvenile Chinook salmon were tested; only those smolts captured in the lower estuary and South Bay, over 73mm in fork length and having characteristic smolt coloration were sampled (N=161). Of these, 63.8% (N=95) originated from outside of the Chehalis Basin (with a majority of the fish (N=74) coming from Willapa Bay), while 14.1% originated from areas beyond the central Washington coast (Puget Sound, the Olympic Peninsula, or the Oregon coast). Based on these results, it is clear that the Grays Harbor estuary serves as a rearing area for juvenile Chinook salmon originating from a broad area of the Oregon and Washington coasts. Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 7

12 Section 1: Introduction 1.1 Purpose and Objectives The juveniles of Pacific salmon spawning in the extensive rivers and streams of Water Resource Inventory Areas (WRIAs) 22 and 23 all must pass through the nearshore habitats in the Grays Harbor Estuary as they emigrate to the ocean. Estuarine environments are extremely productive habitats, and many populations of juvenile salmon spend extended periods of time rearing in this environment. Understanding the extent, timing, and species composition of fish usage in these habitats is a critical component in the development of a salmon restoration strategy for the entire basin. The Grays Harbor Juvenile Fish Use Assessment project is designed to investigate current estuarine habitat use, particularly by juvenile salmonids, and to provide a scientific basis for the selection and prioritization of future salmonid habitat restoration and protection projects within the Grays Harbor estuary. The project had four primary goals at the outset: Determine the abundance, distribution, emigration timing and habitat preferences of juvenile salmonids in the Grays Harbor estuary and tidallyinfluenced portions of its major tributaries Gather information on the distribution, abundance and community structure of non-salmonid fishes in these same areas Use the capture of coded wire tagged salmonids to identify the basin of origin, infer estuarine residence times, and estimate emigration speeds and growth following release from the hatcheries Examine the underlying physical characteristics of the habitat types found in Grays Harbor to understand, and potentially model, the distribution of juvenile salmon in the estuary. This project was proposed, developed, and conducted by the Wild Fish Conservancy with funding provided by the Salmon Recovery Funding Board (SRFB) and the U.S. Fish and Wildlife Service. In 2013, sampling began during the first daylight lowest tide series in March and continued through mid-september (N=574 sets); 498 of these were at core sites, and 76 were at secondary sites. In 2012, sampling began in February and continued until mid-september, and included 570 beach seine sets. Sampling in the first year of this study (2011) began in mid-march and continued through the beginning of October, and included 694 beach seine sets (some additional sets were made to test net capture efficiency, but these catches are not included in the report). Of these, 608 were seine sets at the core sites and 20 were fyke net sets in tidal sloughs Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 8

13 In total, we conducted 1,838 beach seine sets from Our goal was to sample every minus tide series occurring during daylight hours (minus tide series occur at night during the winter months) from early Spring (February or March) through mid- September, wind and weather permitting. Only 5 sampling days were canceled over the three sampling years due to excessive winds, high seas or, in 2011, issues with equipment. 1.2 Study Area Grays Harbor (the Chehalis River estuary) is the second largest estuary in the state of Washington after the Columbia River estuary (Puget Sound is technically considered a fjord ). The Grays Harbor estuary is a bar-built estuary that was formed by the combined processes of sedimentation and erosion caused by both the Chehalis River and the Pacific Ocean (Chehalis Basin Habitat Work Group, 2010). The estuary covers 23,504 hectares at mean high high-water (MHHW) from the mouth at Westport to Montesano, and encompasses the tidally influences lower reaches of the Chehalis, Humptulips, Hoquiam, Wishkah, Johns and Elk Rivers as well as several smaller tributaries (Figure 1). The total drainage area, including all of the above tributaries, is 660,450 hectares, with 79% of the fresh water input from the Chehalis River (Simenstad & Eggers 1981). The system flows are rainfall driven, with peak flows from December- January in an average year, and minimal input from snowmelt in the southern Olympic Mountains (surface drainage occurs primarily through the Satsop River basin). In the inner estuary ( Inner Harbor ), the main river channel splits into north and south channels; the north channel has been dredged for navigation. Vertical salinity stratification, with a salt water wedge typical of estuarine systems, occurs only in the south channel (Simenstad and Eggers, 1981). Between 1900 and 1980, the Grays Harbor estuary had an overall net decrease in tidal wetlands due to extensive diking and filling activities, particularly in the inner portions of the estuary (Boule et al. 1983). A more recent analysis of historical estuarine habitat change detailed a 22% decline in tidal flats (3,493 hectares) due to upland conversion at the mouth of Grays Harbor and along the north channel, an increase in potential eelgrass habitat (1,793 hectares), and an increase in areas below extreme lowwater (ELW) (409 hectares), mainly due to a deepening of the channel near the mouth of the estuary (Borde et al. 2010). Upland logging may have led to an increase in sediment transport to the estuary, resulting in loss of tidal flats due to increased elevation. Dredging for navigation has dramatically deepened the area near the mouth of the estuary, as well as along the north channel, resulting in changes in circulation; wakes from large vessels may have increased channel border erosion and loss of tidal flats in the southern area of the estuary. Historically, the estuary received sediment input from the Columbia River, but the construction of jetties (first in 1900, then in the 1930s) has Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 9

14 reduced this input, which may also explain the loss of tidal flats in the lower estuary (Borde et al. 2010). The northern part of the estuary ( North Bay ) consists of extensive mud flats, most of which are submerged at mean high tide, and has experienced little change. Although much of the basin has been degraded by a combination of logging, channelization, gravel mining, water diversion, road building, diking, dredging, aquaculture, small-scale coal mining, mill effluent, sewage release and pesticide use for aquaculture and cranberry farming (Hiss et al. 1982; Wood & Stark 2002; Smith & Wenger 2001), the area of the lower mainstem Chehalis River, the tidal surge plain (river km 1-17, just east of Aberdeen to the confluence of the Wynoochee River), contains high-quality rearing habitat for juvenile salmon, particularly coho, and has been well studied (Moser et al. 1991; Simenstad et al. 1992; Team 1997; Henning et al. 2006; Henning et al. 2007). The area contains numerous sloughs and tidal channels, a relatively undeveloped floodplain with seasonal inundation, and a riparian forest dominated by older stands of conifers and hardwoods (Ralph et al. 1994). Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 10

15 Figure 1: Location of Grays Harbor (the Chehalis River estuary) in Washington State, U.S.A. Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 11

16 Section 2: Methods 2.1 Habitat Inventory/ Sample Site Selection The tidally influenced areas of the Grays Harbor estuary were divided into six zones: mouth of the estuary, central estuary, north bay, south bay, inner estuary (referred to in the literature as the inner harbor ), and Chehalis River surge plain (see Figure 2). The habitat classification was done using several geographic information system (GIS) layers. The National Wetlands Inventory (NWI) GIS database was used as a basis for our classification (USFWS 2010). The NWI classes were used to group the polygons into subtidal, intertidal, emergent wetlands, shrub/scrub, and forested classes. Then soil data, Shore Zone Inventory data from the Washington Department of Natural Resources (WADNR 2001), and 2009 aerial imagery (USDA 2009) were used to manually subdivide the intertidal polygons into aquatic vegetation bed, mud flat, sand flat, and beach classes. During this step a comprehensive inspection of the classification result was conducted to verify the accuracy and make corrections as needed. Finally, the Shore Zone Inventory data ((WADNR 2001) was used to delineate some preliminary eelgrass habitats (a specific type of aquatic vegetation bed) (Figure 3). Additional locations of eelgrass habitat in the Grays Harbor estuary that were not in any current databases were noted during the 2011 summer sampling, when flows and turbidity decreased, allowing field identification and coordinate fixing via GPS. However, our increasing familiarity with the estuary in 2012 led us to the conclusion that most of the eelgrass habitats identified in the Shore Zone Inventory were poorly defined; unlike the classic eelgrass beds found in Puget Sound (a band of eelgrass along the shore at a particular tidal elevation), the majority of these beds actually contain multiple plant species, visible in mid-summer (but not before). As a result, in 2012 we re-classified eelgrass habitats as aquatic vegetation beds to better reflect the reality of multiple species occurrence; the data for 2011 were re-analyzed to incorporate this change. The habitat areas are included in the habitat maps (Figure 3) and tables used to calculate the percentage of each habitat type (and area) in the Grays Harbor estuary. This same approach was used in Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 12

17 Figure 2: A map of the Chehalis River estuary (Grays Harbor), showing the six zones and locations of the core and secondary sites sampled. The area (in hectares) of each habitat type, by zone, is shown in Table 1, below. These data were used to guide our choices of sampling sites; areas of open water were excluded (although in some cases we sampled the channel margins of some of these areas, which are typically aquatic vegetation beds or sand flats). Mud flats in north bay and the central estuary were sampled at very low or negative tides, when the exposed areas provide a barrier against which the net was drawn, allowing fish to become entrapped. These areas contain large quantities of woody debris, which limited our ability to sample with nets; our efforts to sample mud flats therefore focused on sampling adjacent aquatic vegetation beds. Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 13

18 Figure 3: A map of the Chehalis River estuary showing the six zones and the distribution of the habitat classification types. Table 1: Summary of Grays Harbor intertidal habitat types by zone (in hectares) Habitat Type South Bay North Bay Estuary Mouth Central Estuary Surge Plain Inner Estuary Total % of Total open water , % aquatic bed , % mudflat , % sand flat , % emergent marsh , % scrub/shrub , % forested , % Total 4,169 7,881 1,270 9,310 2,900 4,278 29, % of Total 14.0% 26.4% 4.3% 31.2% 9.7% 14.4% To ensure coverage of the 6 zones and various habitat types, we utilized a twotier sampling system consisting of primary ( core ) sites (sampled fortnightly) and secondary sites ( sampled whenever possible, with a goal of at least once per month). For specific site locations and GPS coordinates, see Appendix 1. Note that certain Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 14

19 habitats (Cobble/Gravel/Sand beaches) occur infrequently in the estuary; our only sites with this habitat type are at Damon Point (Central Estuary) and Half Moon Bay (Estuary Mouth), both near the estuary s outlet. As in 2012, the Charlie Creek site (south shore of the Central Estuary zone) was again sampled in 2013; data for this site from 2011 was provided by Dr. Correigh Greene and colleagues (NOAA/NMFS, Seattle). Some sites, particularly near the estuary mouth ( Half Moon Bay, the only site in the estuary mouth zone), were sampled less frequently due to the restrictions of tides, swell, and weather on our ability to sample without jeopardizing the survival of the fish captured. Two new sites were added in 2013, either to address specific areas of interest (Beardslee Slough, in South Bay, was the proposed site of a new boat launch) or to address logistical sampling issues (e.g. Chinook Eddy, in the Surge Plain, replaced the previous site at Sand Island East, which was filled with large woody debris). One other site from 2012, Mallard Slough (South Bay), was dropped in 2013 because of the addition of new sampling site (Bearsdslee Slough) with similar habitat in the same zone. 2.2 Habitat Area by Salinity Zones Because the various habitat types are not spread evenly throughout the estuary, in 2013 we also created salinity zones to allow us to calculate the areas of the different habitats within these zones (e.g. there is very little forested area in the lower estuary, which is dominated by sand and mud flats). A typical estuary has four salinity zones: polyhaline (18-30 ppt), mesohaline (5-18 ppt), oligohaline (0.5-5 ppt) and limnetic (tidal freshwater, ppt); note that on the Washington coast full seawater (euhaline) typically has a salinity of ppt. The range of surface salinities encountered at the 2013 sampling sites in Grays Harbor is shown in Figure 4. Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 15

20 Figure 4: Box plot showing the range of surface salinity at the sampling sites, 2013 Note that there is a strong seasonal component to the surface salinities that we encountered; early in the sampling year, when rainfall and river flows are elevated (February through May), surface salinities are low at many estuarine sites, but these rapidly increase in July and remain elevated until the fall. Additionally, elevated salinities (relative to nearby, downstream sites) were encountered at the Sculpin Cove site in South Bay due to channel morphology (see Figure 5; most southern region on the map). There is little freshwater input above this site and the tidal channel ends abruptly just below it; a sill encourages complete mixing of the water column, resulting in elevated salinities here even though lower sites (closer to the estuary mouth) have less saline surface waters (in part because the freshwater input from the Elk River joins the main estuary below this site). Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 16

21 Figure 5: Map of Grays Harbor showing the salinity zones used to calculate habitat areas in Section 2.2 The areas of each habitat type were then calculated for the four different salinity zones, in hectares. Table 2: Total area (in hectares) of each habitat type within each salinity zone Area (hectares) Salinity zones Habitat Type High Medium Low Fresh Total Openwater 6, , , Aquatic vegetation bed 6, , Mud flat 3, , , Sand flat , Emergent Marsh , , Scrub/Shrub , Forested , , Total 19, , , , Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 17

22 Table 3: Percent of total area of each habitat in each salinity zone From Table 3, showing the percentage of each habitat type occurring in the different salinity zones, it is apparent that the majority of aquatic vegetation beds (89.3%), mud flats (62.98%) and sand flats (60.5%) occur in the polyhaline ( high ) salinity zone, while the majority of forested (71%) and scrub/shrub (56.1%) habitats occur in the limnetic (freshwater) salinity zone. Emergent marsh habitats are the most evenly spread habitat type, occurring most commonly in the mesohaline (medium) zone (42.4%) but also common in the polyhaline zone (31.7%) and to a lesser extent in the limnetic (16%) and oligohaline (9.8%) zones. The availability of each habitat type within the salinity zones is taken into consideration when comparing the habitat preferences of juvenile salmon via the occurrence and abundance models. 2.3 Field Sampling Methodology Sampling was conducted using fine meshed beach seines which were deployed using a motorized skiff, or set by hand. One end of the net was fixed to shore; the net was then pulled offshore perpendicular to the beach and towed (or walked) back to shore in a 90 arc. At sites with tidal or river currents, we sampled at least twice, in opposite directions, to capture the variability introduced by the current, as daylight and tides allowed. Percentage Salinity zones Habitat Type High Medium Low Fresh Openwater Aquatic vegetation bed Mud flat Sand flat Emergent Marsh Scrub/Shrub Forested We used three different beach seines to sample the various habitats in Grays Harbor and the tidally influenced portions of its major tributaries, each suited to particular habitats (based on depth, current, and substrate). The large seine has 1/8 mesh, is 120 long and 12 deep in the middle of the net and had the heaviest lead lines, allowing use at the deepest sites and in strong currents (intertidal/subtidal fringe or channel margins). The wing of the net that was anchored to the beach tapered to 6, while the other wing had no taper; the large seine sampled an area of m 2 ( hectares) when deployed with this method. Tow lines (bridles) were attached to each end to facilitate deployment. The medium net also has 1/8 mesh and is 100 long and 6 deep uniformly, sampling an area of m 2 ( hectares). We doubled the lead lines to allow this net to fish better in shallow areas of the main estuary, where stronger currents were Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 18

23 common, but soft sediments made the use of the large seine undesirable (the large seine lead line sank into the mud, making retrieval difficult and damaging the fish by rolling them in large clumps of mud upon recovery). Early in the 2012 sampling season, this problem was particularly common at the Stearn s Bluff site, where excessive amounts of fine sediments threatened to result in high mortalities among newly emerged juvenile chum salmon; for this reason, sampling at this site was discontinued until early summer, when flows had removed the finest sediments and average fish size had increased. The small set net has 1/8 mesh, and is 80 long, with no taper, and sampled an area of m 2 ( hectares). This smaller net was rigged with 90 of net along 80 of lead and float line, creating a pocket in the net for holding fish. This net was primarily used in tributaries, the surge plain, or in North Bay (which is extremely shallow). At each large seine sample site two consecutive seine hauls were conducted, with the net anchored to the same spot for each of the sample hauls but the net deployed in opposite directions, to provide a measure of catch variability. Shallow water habitats were sampled using the small seine protocol; at each site three consecutive hauls were conducted whenever possible, moving along the shore so that the same habitat was not sampled twice. Once the nets were closed they were brought into shore for catch processing. All fish captured were enumerated, identified to species, and visually scanned for marks and tags. Juvenile salmonids were also scanned for coded wire tags (CWT) and passive integrated transponder (PIT) tags; all CWT tagged salmon were kept (N=12) in order to determine basin of origin and release date. The first 20 individuals of each species/age class/mark status captured at a site were measured for fork length (mm). Alternate (secondary) sites with the same habitat type were sampled in June and July due to the presence of seals and their pups at our core sampling sites on Goose and Sand Islands; due to the restrictions of the Marine Mammal Act, we could not resume sampling at the core sites until the seals and their pups had moved on. Alternate sites were within several hundred yards of the original core sites. Data Recording/Water Quality Measures For each sampling set, data on date, time of day, net type, percent of net haul utilized in the set (with few exceptions, 100% of the net was utilized; in some cases, such as when currents collapsed the net prematurely, a smaller percentage was fished ), current (ebb, flow, low slack, high slack), habitat, duration of the net set (used in reviewing the data to determine if the net was fished for an unusually long time due to snags, resulting in that particular set s catch being excluded from quantitative analysis) and weather were recorded. At each site temperature and salinity were measured using a water meter (either a WTW model 3400i or a Yellow Springs Instrument Company P40). Tidal heights were back-calculated from the Pro Tides website Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 19

24 using date and time of day to estimate the tide height from the curves (for a complete list of the tide stations used, see Appendix 4). 2.4 Age Class Assignments To differentiate between subyearling and yearling Chinook and coho salmon, we examined the fork length (mm) distributions of catch by species and month, as well as comparing hatchery (marked) and unmarked (presumed wild) salmon. The delineations between the subyearling and yearling fish used in 2013 were the same as those used in 2012 (Table 5). The length classes were quite distinct, with few fish lengths falling in borderline length ranges. Based on our sampling protocol and time limitations in the field to process large catches, only the first 20 of each species/mark status (hatchery or wild, i.e. marked or unmarked) were measured for fork length. To estimate the age class designations of the remaining fish, we calculated the percentage of the catch that were subyearling salmon (based on fork length) and used that result to assign age classes to the remaining fish that were not measured in the field. 2.5 Catch Calculations/ Fish Densities Catch Data All data were originally recorded on a standardized data form in the field; subsequently data from the field forms were entered into a Microsoft Access database for analysis. Catch data were double checked and all data reviewed for QA/QC. These data are summarized as raw catch numbers and catch densities, calculated in hectares (below), and organized by species, sample site and date. Density Calculations At each site at least two consecutive seine hauls were conducted per sampling event, so density was calculated as the summed catch of the net sets (total catch of species y), divided by the sum total area of the consecutive net sets, to get the catch per meter squared. To calculate the density of a given species (or age class of a species) in hectares (1 hectare = 10,000 m 2 ), the formula was: On rare occasions where the net was deployed to a greater or lesser extent than normal, we corrected the standard net area with an estimated fraction of the area sampled. To compare catch densities between sampling zones or habitat types, the above densities in hectares were summed by the appropriate factor (zone or habitat type, by month) to account for biases created by unequal sampling efforts across space or time Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 20

25 and the use of different nets at different sites. This is equivalent to the concept of catch per unit effort (CPUE), with the number of sets made and the area of the net used taken into account, to normalize the catch data by area sampled. Table 4: Mean annual densities (equivalent to CPUE) of Chinook, Chum, and Coho salmon for [ Fall Chinook Chum* YOY Coho Yearling Coho fish/ha (16,951) See Note** (33,537) 26.6 fish/ha (102,237) 14.5 fish/ha (69,403) fish/ha (20,317) fish/ha (29,043) 13.5 fish/ha (64,403) 7.0 fish/ha (102,237) fish/ha (10,341) fish/ha (27,876) 11.1 fish/ha (64,739) 9.0 fish/ha (64,403) The corresponding brood year escapement for each cohort is shown in parentheses. (ha=hectare).] Note: Sampling effort varied between years because of tide and weather restrictions, and the gradual refinement of our sampling strategy and site list. To make valid inter-annual comparisons, we needed to account for these differences; therefore, CPUE was standardized using only our primary sites and months that were fully sampled in all years (April September). *This approach was useful for Chinook and coho since they weren t encountered in any great numbers before April; however, a large portion of the chum outmigration occurred in March, most notably in 2013 (13,025 captured). We chose to include March in the CPUE estimates for chum salmon to compare the relative patterns of salmon abundance in the estuary. **Note that in 2011 sampling was extremely limited before April, so the CPUE estimate for chum salmon (198.5 fish/ha) does not reflect the abundance for that year. Section 3: Salmonid Results 3.1 Salmon Growth/Age Class In general, smaller salmonids ( young-of-the-year (YOY; also referred to as age 0+, or subyearlings) tend to spend more time in estuarine waters and are thus more Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 21

26 dependent on estuarine habitats than larger juveniles ( yearlings ; age 1+), which typically reside in streams for their first year of life prior to smolting, when they rapidly emigrate to sea. These classifications apply mainly to Chinook and coho salmon, who have the most diverse patterns of estuarine usage (Hering et al. 2010; Bottom et al. 2005; Zaugg et al. 1985; Moser et al. 1991); chum salmon migrate directly to the sea shortly after hatching in early Spring and are thus all subyearlings (hatchery chum salmon in the Chehalis Basin are not marked, so all chum were considered unmarked, although in recent years ~5% were of hatchery origin; data from WDFW). No pink or sockeye salmon or bull trout were captured in Steelhead trout, which typically rear in freshwater for 1-3 years (Quinn 2005), were all considered yearlings or older (subadult or adult), as were cutthroat trout. Table 5: Chinook and coho salmon fork length (FL) age class cutoffs (mm) Month Coho YOY Coho yearling Chinook YOY Chinook yearling February March April May June July August September October Juvenile Salmon Size Trends (Fork Lengths) Chinook Salmon [Very few yearling Chinook salmon were captured in any year; for this reason they are excluded from the figures that follow.] An estimated 98% of Chinook salmon released from hatcheries in the basin were adipose fin clipped in (data Pacific States Marine Fisheries Commission, Regional Mark Processing Center). The mean fork length (FL) of both hatchery origin and wild Chinook YOY salmon steadily increased over the course of the study in each year. In 2013, the mean FL was approximately 43 mm in March and increased to 96 mm FL in September (Figure 6), a large increase over the average FL in September of Hatchery Chinook salmon were also significantly larger than their wild counterparts, as expected, in each year (Figure 7). An analysis of variance (ANOVA, Type III sum of squares ) of the fork lengths yielded significant difference between wild and hatchery origin fish, F(1, ) = , p < 0.001; and a significant variation between years, F(2, 18657) = 33.7, p < A post hoc Tukey test showed that for unmarked Chinook, all three years differed significantly at p < Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 22

27 Figure 6: Chinook salmon (YOY) fork lengths (mm), by month Figure 7: Mean fork lengths (FL) of hatchery and unmarked YOY Chinook salmon compared by year Coho Salmon An estimated 2-3% of hatchery YOY coho salmon are marked (total release of 721,966 in 2012); given this low marking rate, all YOY coho salmon were considered unmarked. Over 99% of yearling coho were marked (total release of 2,238,561 in 2012; data from Pacific States Marine Fisheries Commission, Regional Mark Processing Center). The mean length of YOY coho salmon held roughly constant (~40mm) in March and April, 2013, then steadily increased from approximately 52 mm FL in May to approximately 78 mm FL in September (Figure 8). This pattern was consistent between the three years, though there was a significant variation in the mean FL of YOY coho between years F(2, 5642) = 15.76, p < (ANOVA, Type III sum of squares ). A post Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 23

28 hoc Tukey test showed that mean fork length was significantly less in 2011 (p < 0.05) than both 2012 and 2013 (Figure 9a); 2012 was not significantly different from The average fork length of yearling coho salmon was similar in both April and May among unmarked fish and hatchery yearling fish. This trend is driven in part by the timing of hatchery releases, i.e. it does not suggest that these fish failed to grow while in the estuary, but rather that yearling coho are rapidly transiting through the estuary, so different groups of fish were caught in April than in May. An analysis of variance (ANOVA, Type III sum of squares ) of the fork lengths yielded significant variation between years, F(2, 6711) = 16.3, p < 0.001; and a significant difference between wild and hatchery origin fish, F(1,92838) = , p < A post hoc Tukey test showed, that for unmarked coho, the 2011 mean for length was significantly greater (p < 0.05) from both 2012 and 2013; 2012 was not significantly different from 2013 (Figure 9b). For hatchery coho, the 2011 and 2013 mean fork lengths differed significantly at p < 0.05; 2012 was not significantly different from the other two years, lying somewhere in the middle. Figure 8: Coho salmon fork lengths (mm), by month, showing age class designations Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 24

29 Figure 9: Mean fork lengths (FL) of yearling hatchery and unmarked coho salmon compared by year. Chum Salmon As with the other species of juvenile salmon, the mean fork length of juvenile chum gradually increased from March (approximately 42 mm) through May (approximately 50 mm) (Figure 10). Only 2 chum salmon were captured with a FL in excess of 70 mm, fewer than in previous years and perhaps the result of what appears to be an earlier emigration season in 2013 than in Some fish with a FL in excess of 70mm were captured in April and May; because hatchery chum salmon in the Chehalis basin are not marked, it is unclear if any of these fish were of hatchery origin (in the last three years, , the percentage of hatchery chum salmon has been 3, 4, and 9%; WDFW). The mean FL of chum salmon varied significantly between years F(2, 9064) = 91.7, p < (ANOVA, Type III sum of squares ). A post hoc Tukey test showed that mean fork length was significantly smaller in 2013 than either 2012 or 2011 (p<0.05); mean fork length in 2012 and 2011 were not significantly different from each other (Figure 11). Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 25

30 Figure 10: Chum salmon fork lengths (mm), by month (all chum salmon are YOY) Figure 11: Mean fork lengths (FL) of chum salmon (all are YOY) compared between years; asterisk. 3.2 Salmonid Catch Totals (Raw data) Data presented in this section refer to actual salmon catch numbers for ; note that in the later sections of this report that deal with salmon densities by zone and habitat type, catch densities are presented by catch per hectare, and are thus increased by the multiplication factor required since our nets sample only a fraction of a hectare (ha). See section 2.3 for more information had the highest juvenile salmon catch of the three years, with 25,792 salmonids captured (see Table 5), even though sampling effort was roughly equivalent to that of 2012; slightly fewer seine sets were performed in 2013 than in The increase Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 26

31 was largely the result of netting 2,878 additional chum salmon; as in past years, the majority of the salmonids caught were chum. Other increases in catch, as for cutthroat trout (25 more than in 2012), marked Chinook salmon (43 more than in 2012), and marked coho salmon (116 more than in 2012) were offset by decreases in the catch of unmarked Chinook salmon (1,170 fewer than in 2012), steelhead (70 fewer than in 2012), and marked coho salmon (65 fewer than in 2012). This decline in the catch of marked coho salmon (mostly adipose clipped yearlings) continued a three year trend, and represented a decline of 66.3% from 2012 and 74% from The cause of the decline is unknown and does not appear to be the result of variations in the number of coho salmon released from Chehalis basin hatcheries, which were roughly equivalent over the past several years (see comparison of escapement, Section 5.3 below). No bull trout were captured in Table 6: Annual salmonid catch totals for , by species and origin Species/origin 2011 Season Total 2012 Season Total 2013 Season Total Chinook - Unmarked 4,322 6,876 5,706 Chinook - Marked Coho - Unmarked 1, Coho - Marked Chum* 6,810 15,755 18,633 Sockeye Steelhead - Unmarked Steelhead - Marked Rainbow trout Cutthroat trout Bull trout Total 13,149 24,038 25,792 *Note that fewer chum salmon were captured in 2011 due to a later start to sampling As in , chum salmon were already present in the lower estuary in March, 2013 when sampling began, and they were among the most abundant of any juvenile fish in the lower estuary during the first few months of the sampling year (Figures 12, 26). Unlike in past years, the peak chum emigration occurred in March, 2013, rather than in April. By May chum abundances had declined drastically, as they did in , and by June, almost all had exited the estuary (Figure 12). Overall, chum salmon made up 18% of the total fish catch (salmonids and non-salmonids) in Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 27

32 Figure 12: Chum salmon catch by month in Grays Harbor, (*February sampling only occurred in 2012) Chinook salmon were the second most abundant salmonid captured in 2013 (as in ) and were present during all months of the study (Figure 13). Almost all Chinook captured were YOY, and the vast majority were unmarked fish that peaked in abundance earlier in 2013 (April) than in (May), but were present in large numbers from April through July (Figure 14). Overall, chinook salmon (all age classes, hatchery and unmarked combined) amounted to 5.6% of the total fish catch in Figure 13: Chinook salmon catch by month in Grays Harbor, Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 28

33 While caught at an order of magnitude lower abundance, YOY Coho salmon were also present during each sampling month in 2013, as they were in (Figure 14). YOY coho were most abundant from May-July of 2013, with a later peak, in June, than in previous years. As shown below, unmarked fish dominated the catch for Chinook and coho salmon, but hatchery coho salmon (Figure 15) were most commonly caught in April and May of (March and April in 2011), while hatchery Chinook salmon were abundant from June through August, peaking in July. Overall, coho salmon (all age classes, hatchery and unmarked combined) were 0.75% of the total fish catch in Only 15 steelhead were captured in 2013, but the large catch in 2012 was the result of one large set (N=68 hatchery, 13 unmarked) near the mouth of the Humptulips River in April. Slightly more cutthroat trout were caught in 2013 (N=85) than in 2012 (N=65), although the peak catch was in 2011 (N=92). Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 29

34 Figure 14: YOY Coho salmon catch by month in Grays Harbor, (note that the Y-axis scale differs from that of Chinook salmon) Figure 15: Yearling coho salmon catch by month in Grays Harbor, Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 30

35 (note that the Y-axis scale differs from that of Chinook and YOY coho salmon) As Figure 25 shows, salmon make up a relatively small portion of the fish captured during our study. However, early in the year (2012 and 2013), chum salmon can dominate the estuarine fish assemblage among both salmonids and non-salmonids (Figures 16, 26). By May, Chinook came to dominate the salmonid catch in all years (Figure 16), persisting until September; coho salmon make up only a minor portion of the catch in all months, despite being the most numerous in terms of adult returns (Section 5.3); this is an artifact of sampling by beach seine, which does not effectively sample the deeper channels where yearling salmon emigrate. Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 31

36 Figure 16: Monthly catch of salmonids by % salmon species composition, Salmon Distribution and Timing (Densities) Salmon Catch Densities by Zone and Site To visualize the timing of our catches of salmonids in Grays Harbor in 2013, we generated plots showing catch densities (not actual catch) within the zones for each species, age class, and mark status (Figures 17-22). They are presented in order by month to show the seaward emigration of the juvenile salmon; note that the number of plots differ by species/age class/mark status because low catches were not plotted (e.g. few chum in June). There are no plots for yearling Chinook salmon because very few were caught in any year. These same plots for 2011 and 2012 are located in Appendix 3. Chinook salmon Almost all of the Chinook salmon catch consisted of young-of-the-year (YOY) fish, because yearlings prefer deeper water (channels) and so are not captured effectively by beach seining. In 2013, high densities (>400 fish/ha) of YOY Chinook were already present in the Surge Plain, Inner Estuary (including forks the Hoquiam River) and North Bay (near the Humptulips River mouth) in March, with few fish in South Bay (Figure 17). Densities in April were high ( fish/ha) across most of the estuary, with YOY Chinook present at lower densities ( fish/ha) in the Central Estuary and few fish in Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 32

37 the Elk River estuary (South Bay), with higher densities in the Johns River (also in the South Bay zone). YOY Chinook were widespread at moderate to high densities from May through June, and by July the densities of fish in the Surge Plain dropped to near zero as fish moved through to the estuary. By September, the density of YOY Chinook had declined to low levels ( fish/ha) throughout most of the lower estuary except for North Bay, where higher densities persisted ( fish/ha) in the Chenois Creek Flats area. This pattern of emigration was similar to that observed in , although YOY Chinook persisted at higher densities until later in the year in the main estuary in Hatchery Chinook salmon were only detected at low densities (1-50 fish/ha) beginning in May in the Central and Inner estuary, with slightly higher densities ( fish/ha) at the Stearn s Bluff site on the south channel (Central Estuary zone). By June, hatchery Chinook were widespread at low to moderate densities in all zones except South Bay; densities peaked in July across the lower estuary, with several sites in the range of fish/hectare (Figure 18). In August the fish were found at moderate densities ( fish/ha) only at sites near the central estuary, particularly from Goose Island south to the area around the Westport marina, and by September densities had further declined everywhere but at the Chenois Creek Flats site (North Bay). Densities of hatchery Chinook were very low (near zero, except in June) in the Surge Plain throughout the year, suggesting the fish may have been staying in deeper water while quickly emigrating through this zone, avoiding capture in the near-shore beach seines. Coho salmon In proportion to the overall catch, juvenile coho salmon densities were several times smaller than Chinook and chum salmon in all years. The YOY coho, essentially all of which are unmarked in the Chehalis Basin, were present at moderate densities (10-50 fish/ha) in the Hoquiam River system (multiple forks), mouth of the Humptulips River, and South Bay, with slightly higher densities ( fish/ha) in the surge plain in March (Figure 19). Densities in the Hoquiam system were higher than the main estuary through most of the sampling season, with the highest densities (>200 fish/ha) occurring in May- July (slightly earlier than in 2012). Densities in the Central Estuary and Mouth zones were at or near zero through the entire year. This was also the case in the North Bay zone, except for the area near the Humptulips River mouth in March and August (10-50 fish/ha), in direct contrast to 2012, when similar densities were noted near the Humptulips mouth in April and from June-September. YOY coho were present in South Bay at low densities ( fish/ha) in March and April (and June in the Johns River), but absent thereafter. Few were captured in the Surge Plain after April, and there did not appear to be much of an influx of YOY coho from the mainstem Chehalis River via the Surge Plain at any point in the year (Figure 19). Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 33

38 Unmarked, yearling coho salmon were present at a wide range of densities (1-400+) in the Inner Estuary in March (Figure 20). They were widespread in April and May, with the highest densities occurring in the Hoquiam River system (>200 fish/ha) and moderate-high densities present near the Humptulips River mouth (North Bay) and the south channel in May; by June they had exited the estuary and densities were near zero throughout the estuary. Hatchery, yearling coho salmon were detected at very low densities (1-50 fish/ha) in March only in the Inner Estuary and near Chenois Creek (North Bay); in April they were captured at low densities ( fish/ha) only in the Inner Estuary and the Elliot Slough site (Surge Plain) (Figure 21). In May, hatchery yearling coho salmon were more widespread at sites in the Inner Estuary (including the Hoquiam River; fish/ha), North Bay (10-50 fish/ha), Stearn s Bluff (Central Estuary; fish/ha), and one site in South Bay (10-50 fish/ha). Chum salmon Based on their life history, chum salmon fry typically enter an estuary in winter; in the course of this study, they were captured in abundance from early February (in 2012) through late May. In 2013, chum salmon (all are YOY) were already present at very high densities (>400 fish/ha) throughout the estuary when our sampling commenced in March (Figure 22). Unlike in 2011, when chum salmon were largely absent from North Bay, they appeared to utilize North Bay zone habitats extensively in both 2012 and During March and April, chum were also present at high densities in the Surge Plain, Inner Estuary (though at low densities in the Hoquiam River), Central Estuary and South Bay; by May of 2013, their densities had declined throughout the estuary except near the mouth. In 2013, very few chum appeared to originate from the Hoquiam River system, a notable contrast to , when chum were captured in the Hoquiam at high densities. Very few chum remained in the estuary by June in any year. Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 34

39 Figure 17: Density and distribution of unmarked YOY Chinook salmon, 2013 No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 35

40 Figure 18: Density and distribution of hatchery YOY Chinook salmon, 2013 (starting with first month of capture; empty panels equal low/zero catches) No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 36

41 Figure 19: Density and distribution of YOY coho salmon, 2013 No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 37

42 Figure 20: Density and distribution of unmarked, yearling coho salmon, 2013 No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 38

43 Figure 21: Density and distribution of hatchery, yearling coho salmon, 2013 No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 39

44 Figure 22: Density and distribution of chum salmon (all YOY), 2013 No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 40

45 3.4 Coded Wire Tag (CWT) Recoveries/ Genetic Analysis CWT: Coded wire tags (CWTs) were extracted from fish in the lab and codes were read under magnification (40X). Codes were matched to the Pacific States Marine Fisheries Commission Regional Mark Information System (RMIS) database and to the WDFW Wild Salmon Production Evaluation database. The codes were further verified by contact with individual hatcheries and fish biologists with WDFW Wild Salmon Production Evaluation unit. Two yearling coho (one wild and one hatchery origin) and a subyearling Chinook salmon were recovered with CWT in The Chinook salmon was released from the WDFW Forks Creek hatchery in Willapa Bay, the wild coho salmon was tagged in the upper Chehalis River (near RM 52) by the WDFW Wild Salmon Production Evaluation unit, and the hatchery origin coho was released from WDFW Bingham Creek hatchery on the East Fork of the Satsop River. In 2012, six yearling coho salmon (one wild origin) were recovered with CWT. One coho was released from the USFWS Quinault National Fish Hatchery on Cook Creek, three coho from WDFW Bingham Creek hatchery on the East Fork of the Satsop River, and one from the WDFW Humptulips Hatchery. The wild origin coho was tagged in the upper Chehalis River (near RM 52) by the WDFW Wild Salmon Production Evaluation unit. In 2011, 12 yearling coho salmon were recovered with CWT, of which five were wild, tagged by the WDFW Wild Salmon Production Evaluation unit in the upper Chehalis River (near RM 52) and the east fork of the Satsop River. Two hatchery coho originated from the Quinault tribe s Salmon River Fish Culture facility on the lower Queets, four hatchery coho were released from WDFW Bingham Creek hatchery on the East Fork of the Satsop River, and one WDFW Skookumchuck Hatchery. The capture of juvenile salmon in Grays Harbor originating from the Quinault River basin and Willipa Bay demonstrates that the Grays Harbor estuary is utilized by out-of-basin hatchery fish. A 2006 report (Fresh et al. 2006) observed a similar type of pattern for Chinook salmon (use of an area by non-local hatchery salmon) in Puget Sound. Genomics: We hypothesized that naturally produced Chinook salmon from out of basin are also utilizing the estuary, given that these hatchery fish are entering estuarine waters at the same time as some of the wild smolts. This was addressed by taking fin clip samples from Chinook salmon smolts for genetic analysis in 2012, but due to cost restraints not all juvenile Chinook salmon were tested; only those smolts captured in the lower estuary and South Bay, over 73mm in fork length, and having characteristic smolt coloration were sampled (N=161). Genomic DNA was extracted from tissue samples using silica membrane kits (Qiagen DNEasy, Valencia CA). Fish were genotyped at the 13 standardized GAPS microsatellite loci (Seeb et al. 2007). Microsatellite alleles were PCR-amplified using fluorescently labeled primers. PCRs were conducted in 384 well plates in 5 μl volumes employing 1 μl template with final concentrations of 1.5 mm MgCl 2, 200μM of each dntp, 1X Promega PCR buffer, and 0.05units Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 41

46 GoTaq (Promega Corporation) using a touch-down protocol. After an initial two minute denature at 94 C, there were three cycles consisting of 94 C for 30 seconds, annealing at 60 C (temperature stepped down 1 each cycle) for 30 seconds, extension at 72 C for 60 seconds. These were followed by 36 cycles consisting of 94 C for 30 seconds, annealing at 50 C for 30 seconds, extension at 72 C for 60 seconds, then a final 10-minute extension at 72 C. Samples were run on an ABI 3730xl automated DNA Analyzer and alleles were sized (to base pairs), binned using an internal lane size standard (GS500LIZ, Applied Biosystems) and GeneMapper software (Applied Biosystems), and alleles were labeled according to the standardized GAPS nomenclature. Individuals were included in statistical analysis if genotypes were available at 10 or more microsatellite loci. Individual assignment was carried out using the likelihood algorithms employed by the software ONCOR (Anderson et al. 2008) using the GAPS baseline genetic dataset (v.3.5; Seeb et al. 2007). The GAPS baseline database contains collections from populations located from California to Alaska, including some collections added after the initial publication of the database (including Chehalis and Willapa River collections). Power to assign individuals to population of origin was limited because genetic divergence is low among populations on small spatial scales and not all possible source populations are present in the baseline data. However, Chinook populations are genetically related on regional scales (Seeb et al. 2007) generally corresponding to the Evolutionarily Significant Units (ESUs) defined by the National Marine Fisheries Service (NMFS; (Myers et al. 1998)). Thus, assignments were also made to GAPS baseline populations grouped into reporting groups by membership in specific ESUs. In total, 70% of the assignments had a probability of best estimate being true as >0.75. Results from these fin clips, analyzed by the WDFW, became available in June of Based in these results, 63.8% (N=95) of the Chinook salmon sampled originated from outside of the Chehalis Basin (with a majority of the fish (N=74) coming from Willapa Bay), while 14.1% originated from areas beyond the central Washington coast (Puget Sound, the Olympic Peninsula, or the Oregon coast) (see Figure 23). These data show that the Grays Harbor estuary serves as a rearing area for juvenile Chinook salmon originating from a large region encompassing the Oregon and Washington coasts. Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 42

47 Figure 23: Genetic assignments, by population and evolutionarily significant units (ESU), of Chinook salmon sampled in the Grays Harbor estuary, 2012 Section 4: Non-Salmonid Species 4.1 Non-Salmon Species Catch Summary In the course of sampling in 2013 we captured 103,919 non-salmonid fish and encountered 56 species, the highest species total of the three years. The catch included the first capture of Pacific Pomfret (Brama japonica), a species rarely caught inshore. By far the most abundant species was the three-spine stickleback (Gasterosteus aculeatus), making up 42% of the non-salmonid catch, a large increase from 2011 and 2012 (Table 7, Figure 24). The next most abundant species were surf smelt (Hypomesus pretiosus pretiosus; 19% of non-salmonid catch), Pacific staghorn sculpin (Leptocottus armatus; 14% of non-salmonid catch), shiner perch (Cymatogaster aggregate; 14% of non-salmon catch ), unidentified flatfish (most likely English sole (Parophrys vetulus; 8% of non-salmonid catch; we do not attempt to identify flatfish under 30 mm FL due to time constraints in the field). These were followed by two species at roughly equal abundances (3-4% of total non-salmonid catch): snake prickleback (Lumpenus sagitta) and saddleback gunnels (Pholis ornate). Together, the top four species in abundance made up roughly Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 43

48 77% of the non-salmon catch for 2013, very similar to what we observed in 2011 and 2012 (Figure 24). Common species typically occurred in more than one third of the collections and had average density values greater than 100 fish per hectare. Figure 24: Common non-salmonid species shown as percentage of non-salmon catch To visualize the numbers of the most abundant salmonids in comparison with other species commonly captured in the course of this study, we graphed the three-year totals (Figure 25). Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 44

49 Figure 25: Bar plot showing the three year totals of the most abundant fish species caught in the Grays Harbor estuary, Among all fish captured, three-spine stickleback, surf smelt and shiner perch were consistently the dominant species in the estuary. However, saddleback gunnels were more common in 2011 and 2013 than in 2012 (Figure 24), while northern anchovy (Engraulis mordax) were common in 2011 and 2012 but relatively rare in Pacific herring (Clupea harengus pallasi) were only commonly captured in In 2013, two other species increased in abundance- Pacific staghorn sculpin nearly doubled to 14% of the total catch, and snake prickleback made up 4% of the catch, a large increase from previous years that was notable during the sampling season (Figure 24; Table 7). Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 45

50 Table 7: Total non-salmonid catch by species for , in order of annual abundance Common Name Scientific Name Total 2011 Common Name Total 2012 Common Name Total 2013 Surf Smelt Hypomesus pretiosus pretiosus 33,692 3 Spine Stickleback 45,868 3 Spine Stickleback 35,799 3 Spine Stickleback Gasterosteus aculeatus 31,404 Surf Smelt 16,442 Shiner Perch 21,585 Shiner Perch Cymatogaster aggregata 15,029 Shiner Perch 15,656 Staghorn Sculpin 11,525 Northern Anchovy Engraulis mordax 8,239 Northern Anchovy 15,379 Smelt_Juv (50-120) 11,446 Pacific Staghorn Sculpin Leptocottus armatus 6,514 Staghorn Sculpin 10,367 UnID Flatfish 6,589 Pacific Herring Clupea harengus pallasi 4,556 English Sole 5,688 Smelt_pl (<=50) 4,841 Saddleback Gunnel Pholis ornata 4,135 UnID Flatfish 4,186 Snake Prickleback 3,166 English Sole Parophrys vetulus 4,042 Pacific Sand Lance 2,104 Saddleback Gunnel 2,601 Peamouth Mylocheilus caurinus 3,672 Peamouth 2,024 Northern Anchovy 1,715 Unidentified Minnow 1,975 Saddleback Gunnel 1,342 Prickly Sculpin 1,594 Pacific Sand Lance Ammodytes hexapterus 746 Starry Flounder 491 UnID Minnow 968 Starry Flounder Platichthys stellatus 729 Bay Pipefish 474 Starry Flounder 580 Bay Pipefish Syngnathus griseolineatus 685 Prickly Sculpin 466 Bay Pipefish 425 Sand Sole Psettichthys melanostictus 418 Pacific Snake Prickleback 425 Sand_Lance_Juv (50-120) 197 Unidentified Flatfish 414 UnID Sculpin 270 Silver Perch 141 Prickly Sculpin Cottus asper 229 Pacific Herring 74 Red-sided Shiner 103 Pacific Snake Prickleback Lumpenus sagitta 199 Silver Surfperch 46 Sand Sole 86 Northern Pikeminnow Ptychocheilus oregonensis 114 Northern Pikeminnow 41 American Shad 80 Largescale Sucker Catostomus macrocheilus 109 Arrow Goby 39 Arrow Goby 67 Red-sided Shiner Richardsonius balteatus 97 UnID Minnow 37 Anchovy PostLarval (<50mm) 60 Silver Surfperch Hyperprosopum ellipticum 97 UI Larval Fish 34 Torrent Sculpin 51 Bay Goby Lepidogobius lepidus 52 Sand Sole 24 Herring_Juv (50-120) 46 Unidentified Larval Fish 35 Torrent Sculpin 21 Pomfret 37 Pile Perch Rhacochilus vacca 33 Buffalo Sculpin 19 Midshipman ("Toadfish") 36 American Shad Alosa sapidissima 31 Bay Goby 18 Northern Pikeminnow 29 Plainfin Midshipman Porichthys notatus 31 White Perch 17 Smelt_adult (>=120) 28 Buffalo Sculpin Enophrys bison 29 Amerian Shad 15 Pile Perch 16 Black Rockfish Sebastes melanops 25 Pile Perch 14 White Perch 16 Whitefish Prosopium williamsoni 10 Reticulate Sculpin 9 Lingcod 13 Tubesnout Aulorhyncus flavidus 9 Coastrange Sculpin 7 Sharpnose Sculpin 9 Speckled Dace Rhinichthys osculus 8 Largescale Sucker 7 Tubesnout 8 Pacific Ocean Perch Sebastes alutus 7 Riffle Sculpin 7 Sanddab 6 Unidentified Sculpin 7 Whitefish 7 Top Smelt 6 Arrow Goby Clevelandia ios 6 Lingcod 5 Speckled Dace 6 Rock Greenling Hexagrammos lagocephalus 6 Red-sided Shiner 5 Herring_pl (<=50) 5 Striped Seaperch Embiotoca lateralis 5 Speckled Dace 4 Tomcod 5 Cabezon Scorpaenichthyes marmoratus 4 Sanddab 3 Buffalo Sculpin 4 Crescent Gunnel Pholis laeta 4 Sharpnose Sculpin 3 Whitefish 3 Reticulate Sculpin Cottus perplexus 4 Top Smelt 2 Largescale Sucker 3 Torrent sculpin Cottus rhotheus 3 Crescent Gunnel 1 UnID Sculpin 3 Kelp Greenling Hexagrammos decagrammus 2 Kelp Greenling 1 Speckled Sanddab 2 Pacific Tomcod Microgadus proximus 2 Pacific Lamprey 1 Crescent Gunnel 2 White Sturgeon Acipenser transmontanus 2 Plainfin Midshipman 1 Bay Goby 2 Coastrange Sculpin Cottus aleuticus 1 River Lamprey 1 Larval Rockfish 2 High Cockscomb Anoplarchus purpurescens 1 True Cod 1 Lake Chub 2 Largemouth Bass Micropterus salmoides 1 Tubesnout 1 UI Larval Fish 2 Lingcod Ophiodon elongatus 1 White Sturgeon 1 Sand Lance_pl (<=50) 1 Pacific Sardine Sardinops sagax 1 Kelp Greenling 1 Pumpkinseed Lepomis gibbosus 1 Rock Greenling 1 Sharpnose Sculpin Clinocottus acuticeps 1 UnID Cod 1 Reticulate Sculpin 1 Padded Sculpin 1 Striped Perch 1 River Lamprey 1 Pacific Saury 1 Total 117, , , Annual and seasonal composition of the estuarine fish community, In addition to the total abundance of salmonid and non-salmonid fishes, we also investigated the annual versus seasonal component of the estuarine fish community. Chum salmon increased in percent catch from (Figure 26), although our delayed sampling effort in 2011 (due to equipment problems, we started sampling in earnest in April, after many Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 46

51 chum had already emigrated to sea) almost certainly accounts for the lower catch in The percentage catch of surf smelt was highest in 2011, while the catch of shiner perch and Pacific staghorn sculpin peaked in As mentioned previously, northern anchovy were less abundant, both in total numbers and percent of catch, in Figure 26: Annual composition (%) of the eight most abundant fishes, However, there was significant variability in the seasonal catch both within and between years. Surf smelt were the dominant species (by % of catch) through June in 2011, but much less so in (Figure 27). Three-spine stickleback, while present in all months, made up a large percentage of the catch from May-September in , but not in Shiner perch became common in July and August of each year as the water warmed and they began live-bearing their young. In 2011, northern anchovy made up a large percentage of the catch in August; in 2012 they were common in both June and August; in 2013 they were largely absent, though most common in August (Figure 27). The apparent maximum percent catch of chum salmon in April of 2011, as opposed to March in , is again a reflection of sampling effort; we began sampling later in that year and likely missed the peak chum salmon emigration (Figure 27). Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 47

52 Figure 27: Seasonal composition (%) of salmon and the most abundant non-salmonids, With salmonids, which made up roughly 23% of the total catch, removed, slightly different seasonal patterns are more visible (Figure 28). In 2011 surf smelt made up the majority of the percent catch from March-June, while in they were the dominant non-salmonid species only in March and April. Staghorn sculpin were predominant in February and March of 2012 (the only year we could sample in February), a pattern absent in the other years. In mid-summer (July and August) of each year, shiner perch formed a large percentage of the catch, along with the ubiquitous three-spine stickleback. However, the largest catch of stickleback occurred in September of 2011, when they made up roughly 78% of the non-salmonid catch. Northern anchovy showed up in large pulses (25-30% of catch) in August of 2011 and June and August (but not July) of 2012, but made up a noticeably smaller percentage of the catch (~10%) only in August of Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 48

53 Figure 28: Seasonal composition (%) of the seven most abundant non-salmonids, Non-Salmonid Species Abundance: Baitfish and Unusual Catches Three-spine stickleback and shiner perch were particularly abundant and they occurred in almost every month, every zone and every habitat type. Both species reproduced in the estuary and as a result both species were present in various life history stages, which we recorded as adult and juvenile stages only for shiner perch (a viviparous species). Less common were Starry flounder (Platichthys stellatus), Bay Pipefish (Syngnathus griseolineatus), juvenile Sand Lance (Ammodytes hexapterus), Silver Perch (Hyperprosopum ellipticum) and Red-sided Shiner (Richardsonius balteatus). Four species of baitfish were again captured in 2013 (surf smelt, anchovy, herring, sand lance), though, except for surf smelt, at lower abundances than in (Table 7). Northern anchovy made up just 2% of the catch in 2013, and Pacific herring were rarely encountered. English sole and starry flounder were the two most common flatfish collected in 2013, as in past years. Grays Harbor is an important rearing area for juvenile English sole, which utilize the extensive shallow sublittoral and lower littoral habitats (Simenstad & Eggers 1981). English sole were most abundant in South Bay, and their relative abundance diminished from the lower estuary to the surge plain. North Bay had a relatively low abundance of English sole compared with South Bay and the central estuary. In contrast, starry flounder were the most abundant flat fish in the surge plain due to their tolerance of brackish (oligohaline) water. Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 49

54 We captured six top smelt (Atherinops affinis ) in 2013, a species that was first captured in 2012 (N=2). This species is not commonly found as far North as Grays Harbor, preferring the warmer waters of the southern Oregon and northern California coasts. WDFW were notified of these catches, which may represent a species range extension to the North. We also captured a single Pacific saury (Cololabis saira), a highly migratory species common in the nearshore ocean off the Washington coast, inside the Grays Harbor estuary in As mentioned above, our most unusual catch in 2013 was a school of 37 Pacific Pomfret at the Sculpin Cove site in South Bay. The curator of the Burke Museum s fish collection at the University of Washington, Dr. Ted Pietsch, was contacted. He responded via It [Pomfret] is only rarely taken in near-shore waters. The earliest Salish record is based on material collected off Port Townsend in 1882 by James G. Swan who described it as not uncommon off Vancouver Island, and esteemed for its edible qualities (as quoted by Tarleton Bean). Since then, the only additional indication of its presence in our waters is a record from off Mukilteo in central Puget Sound. All known records labeled Strait of Juan de Fuca or Cape Flattery are based on specimens collected far out to sea, well outside of Salish waters. (Bean, 1884b; Jordan and Starks, 1895; Kincaid, 1919; Crawford, 1927b; Mead and Haedrich, 1965; Mead, 1972; Miller and Borton, 1980). Pacific Pomfret from Sculpin Cove, South Bay, Grays Harbor estuary, 2014 Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 50

55 Section 5: Fish Community Modeling 5.1: Site Modeling Physical Variables Due to the size of the Grays Harbor estuary and the number of tributaries entering near the estuary mouth, modeling the system presents interesting challenges in comparison with more traditional, straight line systems where one major river flows into a single estuary before entering the ocean. As opposed to the straight line model, the tributaries of Grays Harbor are radially aligned, with the estuary mouth at the West and (in compass order) the Humptulips (North), Hoquiam (Northeast), Wishkah (NE), Chehalis (East), John s and Elk Rivers (South) (Figures 1, 2). Some of the smaller rivers have estuaries of their own, e.g. the Johns and Elk Rivers. In the absence of a good model of tidal flow for the estuary, the challenge is to relate the sampling areas along each of these axis that, despite being relatively distant in some cases ( as the crow flies ; e.g. Humptulips River sites and Elk River sites are ~12 miles apart), are roughly equidistant from the estuary mouth due to the radial arrangement (Figure 2). A Principal Components Analysis (PCA) of the core and secondary sampling sites physical variables was conducted to determine which characteristics were most influential in relating the sites (McCune & Grace 2002). Initially, separate analyses were conducted for each of the years and for all the years combined; however, the results for each independent year were very similar, so here we present the data for all years combined. Analyzing all the years together allows us to examine broader patterns and include the annual variability expected in this type of study; the assumption is that including more years of data will improve our ability to discern the major components driving fish location and abundance. The analysis was conducted using tidal height, salinity, and water temperature as the main components. The variance is explained primarily by tidal height (45.7%) and salinity (31.2.%), as expected, although these two variables may be autocorrelated because elevation influences the intrusion of salt water. If the plot is rotated, the effect of salinity is still present, but less clear. These investigations of the physical site data provided a preliminary investigation and influenced the creation of the salinity zones in the 2013 report. A matrix of these data (Table 8, Figure 29) will be used to help model the fish community (both salmonids and non-salmonids) for eventual publications, in progress. Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 51

56 Table 8: Results of the Principal Components Analysis (PCA), combined ( TideStag =current direction, TideHt =tide height, and WaterTem=temperature C). ********* PRINCIPAL COMPONENTS ANALYSIS ********** Randomization test. 999 runs.5363 = Seed for random number generator. VARIANCE EXTRACTED, FIRST 3 AXES Broken-stick AXIS Eigenvalue % of Variance Cum.% of Var. Eigenvalue FIRST 3 EIGENVECTORS, scaled to unit length. These can be used as coordinates in a distance-based biplot, where the distances among objects approximate their Euclidean distances Eigenvector attrib TideHt Salinity WaterTem Figure 29: Plot of the Principle Components Analysis (PCA) with three variables Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 52

57 5.2: Salmon Abundance and Occurrence Modeling In order to determine what factors influenced the occurrence and abundance of salmon in Grays Harbor, we constructed separate series of statistical models relating salmon abundance and occurrence to a series of temporal and environmental variables. Models of abundance and occurrence were separated because of the inability to differentiate very low (undetected) abundance from cases where salmon were not present; the inclusion of zeros where salmon were not present in models of abundance could preclude obtaining informative results. Occurrence models were therefore used to understand what factors influenced whether salmon were present at a site on a given occasion (date), and abundance models were used to understand what factors influenced abundance only when salmon were in fact present (e.g., (Mullahy 1986)). For occurrence models we used GLMs employing a logit-link function which assumes a binomial error distribution and relates a binary response (presence/absence in this case) to linear combinations of predictor variables on a logit scale (Nelder & Wedderbu 1972). For abundance analyses we used GLMs employing a log-link function and assuming a negative binomial distribution, which is appropriate for over-dispersed count data, and functions similarly to a Poisson distribution. This analysis related catches of salmon, censored to remove occasions where no salmon were captured, to linear combinations of predictor variables on a log-scale. Separate occurrence and abundance models were constructed for each species, age class, origin (hatchery or unmarked) and year. For each species, age, origin and year, all subsets of up to five predictor variables (Table 9), as well as the full model were tested in a series of additive main effects models. We used a multi-model inference approach to evaluate how well models fit the data. Akaike s Information Criterion (AICc) was calculated to compare and rank the various models (AICc; (Burnham & Anderson 2002)). The difference between the AICc of a candidate model and the model with the lowest score (ΔAICc) was calculated and used to rank models. Models with ΔAICc less than or equal to 3 were considered to have substantial support, while those with values from 4 to 7 had some support and those greater than 7 had little support (Burnham & Anderson 2002). We also calculated Akaike weights (w i ), indicating the strength of evidence supporting i as the best model, and relative likelihoods. Together these metrics were used to identify the best model or model group. All statistical analyses were performed in R (R Team 2012) unless otherwise noted. Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 53

58 Table 9: Variables used in GLM models used to predict salmon occurrence across space and time in the Grays Harbor estuary. Variable Definition Type Mean Range Month Month Factor Habitat Habitat Type* Factor -- #Intertidal pebble, gravel, sand; #Intertidal mixed fines; #Intertidal mixed fines, seasonal aquatic vegetation; #Eulittoral marsh; #Backshore marsh, organic, mixed fines or mud, forested; #Mixed fines or mud channel, forested Salinity Surface Water Salinity (ppt) Continuous Temp Surface Water Temperature ( C) Continuous TideH Tide Height (ft) Continuous * Habitat type was re-defined in 2013 to reflect the scale at which sampling occurs. The new categories, along with the other measured variables, better describe the immediate environment of the organism than the GIS generated habitat types used to classify the estuary at a broad scale. Chinook salmon models The best model of unmarked YOY Chinook occurrence included month, water temperature, and habitat for all years ( ), lending confidence to the variables selected (Table 10). Unmarked Chinook occurrence was higher at temperatures between 11 C and 15 C, and was lower at intertidal pebble, gravel and sand habitats than any other habitat type. Temporal patterns of occurrence varied between years with peaks occurring in June, July and August in 2011, July in 2012 and May, June in Model selection results for occurrence were not well differentiated, with several models having ΔAICc < 3; however, month and water temperature were significant variables in all the best models across years, suggesting that timing and water temperature were key factors influencing Chinook occurrence. The best models of unmarked Chinook abundance included month and habitat in all years (Table 10). The temporal patterns of abundance varied between years: in 2012 Chinook abundance increased through May then steadily declined throughout the rest of the season; in 2013 abundance peaked earlier, in April, before declining; and in 2011 Chinook abundance dropped unexpectedly in June before bouncing back in July, then decreasing through September. Abundance was lower at forested mixed fines/mud channel habitats in 2011 and lower at intertidal pebble, gravel and sand habitats in 2012 and Water temperature and salinity were included in the best model 2011 and 2012, month in 2012 and 2013 and tide height in Unmarked Chinook abundance was negatively correlated with salinity and water temperature, with Chinook essentially absent above 18 C. Model selection results for abundance were better differentiated than for occurrence; the two best models for each year having a ΔAICc < 3. The similar inputs in best models of both occurrence and abundance lend confidence to the importance of the variables selected. Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 54

59 All of the best models of YOY hatchery Chinook occurrence included month and habitat type, while 2011 and 2012 included water temperature, 2012 and 2013 included salinity, and 2013 included tide height (Table 10). Models of hatchery YOY Chinook occurrence were not well differentiated, with three models within ΔAICc = 3, for 2011 and 2013; and four models within ΔAICc = 3, for Hatchery Chinook occurrence is best explained by timing, since the presence of Hatchery Chinook in the estuary depends upon release time. Hatchery releases of fall Chinook salmon took place in May and June during the period of this study, which agrees with the observed peak occurrence in the main estuary. This short window of occurrence, relative to unmarked Chinook, accounts for the inclusion of water temperature in the best models for 2011 and 2012; since water temperature is also correlated with time of year, and hatchery Chinook are absent during cold early season water temperatures. YOY hatchery Chinook occurrence was higher in several habitat types including intertidal mixed fines, intertidal mixed fines/seasonal aquatic vegetation, and intertidal pebble/gravel/sand; all intertidal habitats which occur in the main estuary. This corresponds with a rapid downstream migration from the hatchery into the main estuary where the smolts disperse across a large area. Consequently, hatchery Chinook occur for a shorter period of time in the upper estuary, and occur more often in the lower estuary. Models of hatchery YOY Chinook abundance were not well differentiated, with nine of the twelve best models having ΔAICc < 3, and high relative likelihoods of being the best model. All of the best models of YOY hatchery Chinook abundance included month while the other variables differ between years (Table 10), which lends confidence to the selection of month as an explanatory variable, and indicates that hatchery Chinook abundance is an artifact of release timing. Peak abundance occurred in July (2011), May and July (2012) and July and August (2013). In addition to the explanatory variable month, YOY hatchery abundance was negatively correlated with water temperature in 2013, negatively correlated with tide height in 2012, and greater in mixed fines/mud channel/forested habitats in Table 10: Model selection results for GLM models relating Chinook salmon abundance and occurrence to time of year, and environmental variables. The four best models including the full model, are listed from most plausible (ΔAICc=0) to least plausible. Models are separated by year, age class and by hatchery/unmarked origin. Model 1 AICc ΔAICc Relative likelihood Akaike weight (w i ) R 2 Cumulative Weight Unmarked YOY Occurrence 2011 Month + Temp + Habitat Month + Temp + Habitat + Salinity Month + Temp + Habitat + TideH Month + Temp + Habitat + Salinity + TideH Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 55

60 Unmarked YOY Occurrence 2012 Month + Temp + Habitat Month + Temp + TideH Month + Temp + Habitat + Salinity Month + Temp + Habitat + TideH Unmarked YOY Occurrence 2013 Month + Salinity + Temp + Habitat Month + Salinity + Temp Month + Salinity + Habitat Month + Salinity + Temp + Habitat + TideH Unmarked YOY Abundance 2011 Month + Salinity + Temp + Habitat Month + Salinity + Temp + Habitat + TideH Month + Salinity + Temp Month + Salinity +Temp + TideH Unmarked YOY Abundance 2012 Month + Salinity + Temp + Habitat + TideH Month + Salinity + Temp + TideH Month + Salinity +TideH Month + Salinity + Temp + Habitat Unmarked YOY Abundance 2013 Month + Salinity + TideH + Habitat Month + Salinity + TideH + Habitat + Temp Month + Salinity + TideH Month + Salinity + TideH +Temp Hatchery YOY Occurrence 2011 Month + Habitat + Temp Month + Habitat + Temp + Salinity Month + Habitat + Temp + TideH Month + Habitat + Temp + Salinity + TideH Hatchery YOY Occurrence 2012 Month + Habitat + Salinity +Temp + TideH Month + Habitat + Salinity + TideH Month + Habitat + Salinity Month + Habitat + Salinity + Temp Hatchery YOY Occurrence 2013 Month + Habitat + Salinity +TideH Month + Habitat + Salinity + Temp + TideH Month + Habitat + Salinity Month + Habitat + Temp + TideH Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 56

61 Hatchery YOY Abundance 2011 Month + Habitat + Temp + Salinity Month + Habitat + Temp Month + Habitat + Temp + Salinity + TideH Month + Habitat + Salinity Hatchery YOY Abundance 2012 Month + TideH Month + TideH + Salinity Month + TideH + Temp Month + TideH + Salinity + Temp Hatchery YOY Abundance 2013 Month + Salinity + Temp Month + Salinity Month + Salinity + Temp + TideH Month + Salinity + TideH Yearling Chinook occurrence and abundance were not modeled since few were encountered. Coho salmon models The best models of unmarked YOY coho salmon occurrence included salinity and habitat type across all years (Table 11). Unmarked YOY coho occurrence was negatively correlated with salinity, with occurrence declining quickly at salinities above 5 ppt, and coho essentially absent above 20 ppt. Occurrence of unmarked YOY coho was greater in mixed fines or mud channel/forested sites and backshore marsh/forested sites, habitats which are associated with lower salinities. Model selection results for 2011 and 2012 were not well differentiated, but 2013 models were modestly well differentiated (two best models within ΔAICc = 3). The best models of unmarked YOY coho abundance all included salinity, supporting the selection of this variable as a strong predictor of abundance. YOY coho abundance was negatively correlated with salinity in all years, positively correlated with mixed fines or mud channel/forested habitats in 2012, and positively correlated with tide height in All of the best models included salinity, suggesting that osmoregulation was a dominate factor influencing unmarked YOY coho occurrence and abundance. Model selection results were modestly well differentiated, with just two models within ΔAICc = 3, for 2011 and 2013, and three models within ΔAICc = 3, for The best models of unmarked yearling coho salmon occurrence all included month, while other explanatory variables including water temperature, salinity, habitat type, and tide height, varied between years (Table 11). The inclusion of month in all the best models supports the selection of this variable as a strong predictor of occurrence corresponding with a rapid period of smolt emigration: occurrence was highest in April and May before dropping rapidly in June, with wild yearling smolts essentially absent from the sampling sites by July. In addition to month, occurrence was positively correlated with salinity and negatively correlated with temperature in 2011; and positively correlated with two habitat types - #intertidal mixed fines/seasonal aquatic Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 57

62 vegetation and #mixed fines/mud channel/forested - in Models of unmarked yearling coho occurrence were poorly differentiated, with multiple models having ΔAICc < 3. The best models of yearling unmarked coho abundance varied greatly between years: in 2011 yearling unmarked coho abundance was negatively correlated with water temperature and tide height; in 2012 abundance was negatively correlated with water temperature and positively correlated with the months April and May; and in 2013 abundance was negatively correlated with salinity. Models of unmarked yearling coho abundance were modestly well differentiated in 2011 and 2012 (two and three models having ΔAICc < 3 respectively), while 2013 models were very poorly differentiated with eight models having ΔAICc < 3; complicating interpretation and inference. Models of hatchery yearling coho abundance were not generated due to the small number of occasions in which they were encountered. Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 58

63 Table 11: Model selection results for GLM models relating coho salmon occurrence and abundance to time of year, and environmental variables. The four best models including the full model, are listed from most plausible (ΔAICc=0) to least plausible. Models are separated by age class and by hatchery/unmarked origin. Model 1 AICc ΔAICc Relative likelihood Akaike weight (w i ) R 2 Cumulative Weight Unmarked YOY Occurrence 2011 Salinity + Habitat + Temp Salinity + Habitat Salinity + Habitat + Temp + TideH Salinity + Habitat + Temp + Month Unmarked YOY Occurrence 2012 Salinity + Habitat + Temp Salinity + Habitat Salinity + Habitat + Temp + TideH Salinity + Habitat + TideH Unmarked YOY Occurrence 2013 Salinity + Habitat + Temp + TideH Salinity + Habitat + Temp Salinity + Habitat + Temp + Month Salinity + Habitat + Temp + TideH + Month Unmarked YOY Abundance 2011 Salinity + Temp + TideH + Month Salinity + Temp + Month Salinity + Temp Salinity + TideH + Month Unmarked YOY Abundance 2012 Salinity + Habitat + TideH Salinity + Habitat Salinity + Habitat + TideH + Temp Salinity + Habitat + Temp Unmarked YOY Abundance 2013 Salinity + Temp + Month Salinity + Temp + Month + TideH Salinity + Temp + Month + Habitat Salinity + Temp + Month + Habitat + TideH Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 59

64 Unmarked Yearling Occurrence 2011 Month + Temp + Salinity Month + Temp + Salinity + TideH Month + Temp + Habitat Month + Temp + Habitat + TideH Unmarked Yearling Occurrence 2012 Month + Temp Month + Salinity Month + Temp + Salinity Month Unmarked Yearling Occurrence 2013 Month + Habitat + Salinity +TideH Month + Habitat + Salinity Month + Habitat + Salinity + Temp + TideH Month + Habitat Unmarked Yearling Abundance 2011 Temp + TideH Temp + Salinity + TideH Temp Temp + Month + TideH Unmarked Yearling Abundance 2012 Month + Temp + Salinity Month + Temp Month + Temp + Salinity + TideH Month + Temp + TideH Unmarked Yearling Abundance 2013 Salinity Salinity + Habitat Salinity + TideH Salinity + Habitat + TideH Yearling hatchery coho occurrence and abundance were not modeled since few were encountered. Chum salmon models The best models of chum salmon occurrence all included month, while other explanatory variables, including water temperature, salinity, habitat type, and tide height, varied in significance between years (Table 12). The inclusion of month in all of the best models supports the selection of this variable as a strong predictor of occurrence: chum occurrence was high through April before dropping rapidly in May, with juvenile chum essentially absent from the sampling sites by June. Models of chum occurrence were poorly differentiated, with multiple models having ΔAICc < 3. This may be due to the relative strength and contribution of month as a predictor of chum Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 60

65 occurrence in all the best models; sampling month as a single variable model explained a large portion of the variation in chum occurrence (R 2 = 0.63, 0.71 and 0.72 in 2011, 2012 and 2013 respectively). Of the other explanatory variables selected in the best models, chum salmon occurrence was positively correlated with salinity in 2012 and water temperature in The best models of chum salmon abundance included month in all years, while habitat type was selected in all the best models for 2011 and 2012, and salinity in all the best models for 2013 (Table 12). The timing of the chum outmigration drove the selection of month in all the best models, with peak abundance taking place in April in 2011 and 2012, but occurring earlier in 2013, in March. Model selection results were not well differentiated, with three models within ΔAICc = 3, for 2011 and 2013; and six models within ΔAICc = 3, for 2012; but once again this may be due to the relative strength and contribution of month as a predictor of chum occurrence in all the best models. Chum abundance in 2011 and 2012 was positively correlated with intertidal habitats which are most common in the main estuary: intertidal mixed fines, intertidal mixed fines/seasonal aquatic vegetation, and intertidal pebble/gravel/sand. Chum abundance was positively correlated with salinity in Salinity and habitat may confound each other to some extent, since juvenile chum make a rapid outmigration from their natal rivers into the main estuary where salinity is greater and intertidal habitats prevail. Table 12: Model selection results for GLM models relating chum salmon occurrence and abundance to time of year, and environmental variables. The four best models including the full model, are listed from most plausible (ΔAICc=0) to least plausible. Model1 1 AICc ΔAICc Relative likelihood Akaike weight (w i ) R 2 Cumulative Weight Unmarked YOY Occurrence 2011 Month + Temp + Salinity Month + Temp Month + Salinity Month + Salinity + Temp + TideH Unmarked YOY Occurrence 2012 Month + Salinity + TideH Month + Salinity Month + Salinity + Temp + TideH Month + Salinity + Temp Unmarked YOY Occurrence 2013 Month + Habitat + Temp Month + Habitat + Temp + Salinity Month + Habitat + Temp + TideH Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 61

66 Month + Habitat + Salinity + Temp + TideH Unmarked YOY Abundance 2011 Month + Habitat + Temp Month + Habitat + Salinity Month + Habitat + Temp + Salinity Month + Habitat + Temp + TideH Unmarked YOY Abundance 2012 Month + Habitat + Temp + TideH Month + Habitat Month + Habitat + Temp Month + Habitat + Temp + Salinity + TideH Unmarked YOY Abundance 2013 Month + Salinity + Temp Month + Salinity Month + Salinity + Temp + TideH Month + Salinity + TideH All chum were assumed to be wild due to the inability to differentiate hatchery chum, which are not externally marked. 5.3: Escapement estimates for Grays Harbor salmon The latest escapement numbers, not yet finalized for 2013 adult returns, are listed below (Table 13). Coho salmon had high returns in , and marginally high returns in Historically, coho salmon are the most abundant Pacific salmon species in the Chehalis River/Grays Harbor system, though returns are highly variable, as seen in Figure 30. Fall Chinook salmon escapement was normal in 2010 and 201 and high in Chum salmon returned with high escapement in all years of this study. Note that these rankings are relative to the recent past (1969); historically, salmon abundances in the Grays Harbor system were substantially greater and current stock numbers are depressed, though no salmon species are listed under the Endangered Species Act at present (bull trout, which are protected, are in the char family). While the (relatively) strong escapement numbers are good news for Pacific salmon, the ecosystem, and the human enterprises that rely upon them, they complicate modeling efforts. In an ideal study situation we would sample juvenile salmon after years of low, normal, and high escapement in order to better understand how density dependence may affect habitat preference and utilization, with the assumption that high numbers of adult returns lead to an abundance of juveniles the following year/s. For example, in years of low juvenile abundance, we may have observed salmon becoming more selective in their habitat utilization, emigration timing, and residency. Relatively high numbers of juvenile salmon may force utilization of less ideal habitats, faster emigration to sea, and potentially shorter residence times within the estuary if food and other resources become limited by density dependence. Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 62

67 Figure 30: Annual escapement estimates for salmon in Grays Harbor from Table 13: Escapement values defining the interquartile range, or normal productivity year, for fall Chinook, coho and chum salmon Escapement Coho Fall Chinook Chum 1 st Quartile 25,400 8,190 11,101 3 rd Quartile 64,348 17,025 24, escapement 64,739 (~high) 10,341 (normal) 27,876 (high) 2011 escapement 64,403 (~high) 20,317 (high) 29,043 (high) 2010 escapement 102,237 (high) 16,951 (normal) 33,537 (high) 2009 escapement 69,222 (high) Note: Values that fall above or below the interquartile range are considered high or low productivity years. Escapement estimates for the brood years that produced most of the juvenile salmon captured in are shown in red. Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 63

68 Section 6: Synthesis and Recovery Priorities Estuaries have been shown to enhance the survival of juvenile salmon by providing: (1) habitat for overwintering juvenile salmonids forced downstream during high river flows (Sommer et al. 2001; Simenstad et al. 1992; Henning et al. 2007); (2) complex low-velocity refugia such as off-channel sloughs and large woody debris (LWD) (Gonor et al. 1988; Swales & Levings 1989; Wick 2002; Henning et al. 2006; Simenstad & Eggers 1981; Henning et al. 2007); (3) time for migrating juveniles to adapt physiologically to sea water (Folmar & Dickhoff 1980; Healey 1980; Levy & Northcote 1982; Iwata & Komatsu 1984; Zaugg et al. 1985); (4) opportune feeding conditions as drift insects and other prey items are trapped and concentrated due to flow reversals (Tschaplinski 1987; Eggleston et al. 1998; Simenstad & Eggers 1981); (5) settling of suspended sediments and detritus, which can fuel soft-sediment habitat formation and detritus-based food webs exploited by salmon (Simenstad et al. 1982; Maier & Simenstad 2009; Thorpe 1994; Bottom et al. 2005). (6) a refuge from piscivorous and avian predators, due in part to the often turbid water resulting from river flows and tidal action (Gregory & Levings 1998; De Robertis et al. 2003; Simenstad et al. 1982; Thorpe 1994). The results from our sampling indicate a wide range of habitat utilization by the various species and age classes of salmonids found in Grays Harbor. In 2013, clear growth trends were again observed for YOY Chinook, coho and chum salmon, indicating that the estuary is functioning as a refuge for these fish as they physiologically mature and prepare to enter the ocean. Individual points are discussed below. 6.1 Salmonid Spatial and Temporal Habitat Usage Life history variation has been recognized as a critical factor in resilience - the ability of native stocks to persevere and recover from perturbations in abundance, habitat and climate variability- among Pacific Northwest salmonid stocks (Greene et al. 2010; Bottom et al. 2005; Simenstad et al. 1982). In many systems with hatchery production, the range of life histories has been reduced via the selection of a limited diversity of broodstock, particularly with regard to run timing. In most systems, this has resulted in pulses of emigrants reaching the estuarine rearing habitats at the same time, which may create artificially heightened competition for estuarine habitat. While meeting our objective of documenting temporal and spatial habitat usage by salmonids in Grays Harbor, a secondary goal is to identify alternative estuarine life history strategies that are still extant in the Chehalis basin and may be important both for the restoration Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 64

69 of salmon populations in the watershed and their ability to persevere under the predicted changes in climate. Chinook Salmon Overall, juvenile unmarked Chinook salmon catch was lower in 2013 (N= 5,706) than 2012 (N= 6,876) and higher than 2011 (N= 4,322). Catch per unit effort (CPUE) for each year was as follows: 118 fish/ha (2011), 201 fish/ha (2012) and 141 fish/ha (2013). The capture of hatchery Chinook in 2013 (N= 504) was higher than in 2012 and 2011 (N=461 & 397, respectively). Chinook salmon were the second most abundant salmonid captured (after chum salmon) and were present during all sampling months in all three years. Very few yearling Chinook salmon were caught throughout the study, a result that closely resembles that of an earlier study in the Chehalis basin (Deschamps et al. 1970). Yearling Chinook salmon have previously been reported to reside in deeper dendritic tidal or river channels (Zaugg et al. 1985; Thorpe 1994; Fresh et al. 2005) that are not effectively sampled by beach seining, which may explain our low catches. The temporal patterns of abundance varied between years: in 2013 Chinook abundance peaked in April before steadily declining through the rest of the season; in 2012 abundance increased through May then steadily declined throughout the rest of the season; and in 2011 Chinook abundance dropped unexpectedly in June before bouncing back in July, then decreasing through September. Hatchery YOY Chinook were present in the estuary mainly from June through August (though present in May and September), slightly later than in 2011, when they were present from May through September. Unmarked YOY Chinook salmon where widely dispersed throughout the estuary during late spring and early summer and showed a clear seaward migration pattern as the sampling season progressed (Figure 17). However, the regression modeling shows that although abundance decreased later in the year, occurrence did not YOY Chinook salmon continued to utilize estuarine habitats into the fall. The timing of catch in both years of this study closely follows that of Simenstad and Eggers (1981), who reported catches of YOY Chinook salmon nearly year-round in Grays Harbor, and of Deschamps et al. (1970), who had their peak Chinook catch in May. This suggests a variety of Chinook salmon life histories are present in the basin, and, particularly for unmarked Chinook, estuarine residence times are longer than for the other salmonid species. Unmarked YOY Chinook salmon steadily increased in fork length from February through September (Figure 6; see also appendices 7 and 8 for previous years data). They were notably less common at intertidal pebble, gravel and sand habitats, and both their presence and abundance were negatively correlated with temperature. Hatchery yearlings were significantly larger (FL) than their unmarked peers in each month from May to August. YOY Hatchery Chinook abundance is best explained by timing, since the presence of Hatchery Chinook in the estuary depends upon release time. Hatchery releases of fall Chinook salmon took place in May and June during the period of this study, which agrees with the observed peak occurrence in the main estuary. YOY hatchery Chinook occurrence was higher in several habitat types including intertidal mixed fines, Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 65

70 intertidal mixed fines/seasonal aquatic vegetation, and intertidal pebble/gravel/sand; all intertidal habitats which occur in the main estuary. These patterns reflect a more direct downstream migration into the main estuary; hatchery YOY Chinook salmon were present for a shorter period of time than unmarked YOY Chinook. Coho Salmon Juvenile unmarked coho salmon catch was slightly higher in 2013 (N= 810) than 2012 (N= 694) but much lower than 2011 (N= 1,370). The capture of yearling hatchery coho in 2013 (N= 33) was much lower than previous years (N= 129 & 98, in 2011 & 2012 respectively). Unmarked YOY coho were present throughout the sampling season, though at very low abundance in March and September; marked coho were only present March, April and May. Previous studies in Grays Harbor reported YOY coho captures from March through October, peaking in mid-april through mid-june (Brix 1981; Tokar et al. 1970). The abundance of unmarked coho peaked in June of 2013, and the YOY were caught mainly in the inner estuary in all months, particularly in the Hoquiam River system (Figure 19). Yearling coho, though present at lower densities, were more dispersed through the central estuary, South Bay, and North Bay, with a pattern of input from the Humptulips River from March-June (Figures 20, 21). The mean fork length of YOY coho salmon steadily increased during the study from April to September (Figure 8; see also appendix 7 for previous years data); there was little increase in mean fork length from February to April. Hatchery yearlings were significantly longer (FL) than their wild counterparts in both April and May. However, the average fork length of hatchery yearling coho decreased slightly from April through May (especially evident in the 2011 data), corroborating the evidence that yearlings did not reside for long periods of time within the estuary (the fish captured in May did not decrease in size; rather, new pulses of smaller coho from upstream made up the catch). This finding was also consistent with studies elsewhere that have observed larger coho smolts, which may be more ocean ready, migrating before smaller smolts (Irvine and Ward 1989). Coho salmon occurrence and abundance was negatively correlated with salinity; when salinity exceeded 5ppt their occurrence declined quickly, and above 20ppt they were essentially absent. Occurrence of unmarked YOY coho was greater in mixed fines or mud channel/forested sites and backshore marsh/forested sites, habitats which are associated with lower salinities. This suggests that YOY coho are rearing in the estuary for extended periods of time (unlike the yearlings, which quickly migrated to sea) and are not yet fully able to osmoregulate in salt water; it is likely that many of these fish will not smolt until 2013 (the nomad lifestyle alluded to in other studies (Koski 2009; Bell & Duffy 2007)). Studies conducted in the lower Chehalis River in the late 1960 s reported capturing coho in their third year (by scale analysis), again suggesting that historically, multiple life histories existed within the basin (Deschamps et al. 1970), although no coho salmon large enough to be three year olds were captured in 2011, 2012 or Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 66

71 Chum Salmon More juvenile chum salmon (all YOY) were captured in 2013 (18,633; Table 4) than either of the previous years, particularly than in 2011 because we commenced sampling in late March that year, and missed a large portion of the chum outmigration. Chum salmon were present from March to June (N=4), at which point all chum salmon had migrated to sea, in keeping with their life history (Wright 1973; Tokar et al. 1970; Brix 1981; Simenstad & Eggers 1981). Previous research in the Chehalis River indicates that the chum emigration is underway as early as January in most years (Deschamps et al. 1970). As with the other species of juvenile salmon, the mean fork length of juvenile chum gradually increased from March (approximately 42 mm) through May (approximately 50 mm) (Figure 11; see also appendix 7 for previous years data). Only 2 chum salmon were captured with a FL in excess of 70 mm, fewer than in previous years and perhaps the result of what appears to be an earlier emigration season in 2013 than in The overall catch of chum salmon was higher in 2013, so a possible explanation is that the higher abundance of chum salmon in the estuary may have resulted in more competition, encouraging the chum to move to sea earlier. The mean FL of chum salmon captured in 2011 was also significantly lower (p<0.001) in 2013 in comparison with both 2011 and Chum were widespread throughout the estuary in March and April, and by May they were at much lower densities in the surge plain as the fish pushed through to the estuary (Figure 22). Peak abundance occurred in March in 2013 (compared to April in 2012) and then decreased quickly. The regression models for chum salmon indicate that timing was the most important factor explaining abundance and occurrence in the estuary. In addition to timing, abundance was positively correlated with intertidal habitats which are most common in the main estuary: intertidal mixed fines, intertidal mixed fines/seasonal aquatic vegetation, and intertidal pebble/gravel/sand. This pattern of estuarine use may reflect the inherent changes in productivity and the relative growth opportunities of the estuary versus the nearshore ocean early in the year. Several studies have pointed out the especially large contribution of harpacticoid copepods in the diets of juvenile salmon (Naiman & Sibert 1979; Mayama & Ishida 2003) and the residence period of chum salmon may be driven by the relative abundance epibenthic prey (Wissmar & Simenstad 1988) during the late spring. Trout Only 15 steelhead trout were captured in The 2012 catch was far higher (N=85), but the majority of those were captured in one set most likely (based on nearly identical FL) consisted of a single hatchery release group (N=68 hatchery, 13 unmarked). In 2011, 24 steelhead were captured; overall, the low catch numbers preclude any comparison of their habitat preferences. Slightly more cutthroat trout were caught in 2013 (N=85) than in 2012 (N=65), although the peak catch was in 2011 (N=92). Though cutthroat trout were encountered infrequently, enough were captured over time to observe some patterns of estuary use. Cutthroat densities were highest at Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 67

72 scrub/shrub cover and emergent marsh sites, although some were also caught in every habitat except cobble/gravel/sand beaches and sand flats. Their densities closely aligned in space and time with those of YOY Chinook salmon, suggesting possible predation. Our catches of cutthroat trout demonstrate that this species is present in Grays Harbor through much of the year (March to September), though they were most commonly encountered from April to June. No bull trout were captured in 2013; previously, seven had been captured (3 in 2011, 4 in 2012) and sampled for genetics (samples submitted to USFWS) before being released. 6.2 Analysis of estuarine modifications (for restoration) In addition to generating a framework by which to prioritize future habitat restoration projects in the Grays Harbor estuary, a goal in 2013 was to conduct an assessment of the type and extent of habitat alterations in the estuary. This assessment looked at the estuary as a whole to compile historical habitat alterations (Figure 31), and can also be used at finer scale to aid in the planning and development of restoration projects (for example, see Figure 32). Overall the largest human alterations to the estuary involve diking and/or elevated roads, particularly along the South shore and within South Bay and the Johns River estuaries. An additional area of intense diking is on the northeastern shore of North Bay, between Chenois Creek and the mouth of the Humptulips River. These areas are prime candidates for habitat recovery, particularly in the face of predicted sea level rise (SLR). In 2014, with grant support from the Rose Foundation, we continued sampling in the Surge Plain and the lower Chehalis River upstream to Porter, WA. The goal of this effort is to characterize juvenile fish use of the lower river, as well as to explore areas that will become increasingly important for juvenile salmon and other fishes as SLR impacts (and potentially destroys the tidal swamp in) the existing Surge Plain. Compilation of these data continues and will be summarized in a separate report outlining habitat restoration and preservation priorities for the Grays Harbor estuary in the fall of Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 68

73 Figure 31: Map showing habitat alterations in Grays Harbor, by modification type Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 69

74 Figure 32: Chenois Creek area habitat alterations, North Bay Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 70

75 Completing a seine set, Elk River Flats, South Bay, 2013 Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 71

76 Acknowledgements A large number of people were involved in the sampling effort for this three year project and we are indebted to them for their assistance (and persistence) in the field: Aaron Jorgenson, Adrian Tuohy, and Frank Staller (Wild Fish Conservancy), Emily Coba, Elanor Wolff, Becky Winnick, Casey Pruitt, Caroline Walls, Sarah Farley, Derek Brady, Rhoda Green, Eliana Sigelman, Robert Wadsworth, Tanner Scrivens (DNR), Eric Delvin (The Nature Conservancy), Rory Donovan, Jessica Jang, Molly Gorman, Christian Sartin, Megan Lang, Tanya Budiarto, Andrew Muchlinski, and Matt Bus, among others. We are grateful to Thomas Beuhrens (WDFW; formerly of WFC) for assistance with field work and regression modeling in the R statistical package, Mike Scharpf (WDFW) for assistance in locating and compiling salmon escapement data, and the WDFW for the loan of a CWT wand for the sampling seasons. Thanks also to DNR staff from the Quinault tribe for assistance with determining the origin and time of release for the coded-wire tagged coho salmon released from their nation. We wish to thank the commercial fishing community in Westport for advice and knowledge on the distribution and historical trends of fisheries in the region, as well as hazards to navigation. Finally, we wish to thank the numerous private landowners, Grays Harbor Audubon Society, the Cascade Land Conservancy, Washington State Parks, WDFW, Washington DNR, the Port of Grays Harbor and the cities of Aberdeen and Hoquiam for making much of this work possible by allowing us to access sampling sites on their property. This project was funded by the Grays Harbor county Salmon Recovery Funding Board and the U.S. Fish and Wildlife Service and is available online as a pdf (as well as other project mapping products and summaries) at the Wild Fish Conservancy s website: Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 72

77 References Anderson, E.C., Waples, R.S. & Kalinowski, S.T., An improved method for predicting the accuracy of genetic stock identification. Canadian Journal of Fisheries and Aquatic Sciences, 65(7), pp Bell, E. & Duffy, W., Previously Undocumented Two-Year Freshwater Residency of Juvenile Coho Salmon in Prairie Creek, California. Transactions of the American Fisheries Society, 136(4), pp Borde, A.B. et al., Geospatial Habitat Change Analysis in Pacific Northwest Coastal Estuaries. Estuaries, 26(4), pp Bottom, D.L. et al., Salmon at River s End: The Role of the Estuary in the Decline and Recovery of Columbia River Salmon, Boule, M.E., Olmsted, N. & Miller, T., Inventory of wetland resources and evaluation of wetland management in Western Washington. Brix, R., studes of juvenile salmonids in rivers tributary to Grays Harbor, Washington, Olympia: Washington Department of Fisheries. Brix, R., Data report of Grays Harbor juvenile salmon seining program, , Olympia: Washington Department of Fisheries. Burnham, K.P. & Anderson, D.., Model selection and inference: a practical information theoretical approach, New York: Springer-Verlag. Deschamps, G., Wright, S.G. & Watson, R.E., Fish migration and distribution in the lower Chehalis River and upper Grays Harbor W. D. of Fisheries, ed., Technical, pp Deschamps, G., Wright, S.G. & Watson, R.E., Fish migration and distribution in the lower Chehalis River and upper Grays Harbor W. D. of Fisheries, ed., Technical, pp Duffy, E.J. et al., Ontogenetic Diet Shifts of Juvenile Chinook Salmon in Nearshore and Offshore Habitats of Puget Sound. Transactions of the American Fisheries Society, (January 2012), pp Duffy, E.J. & Beauchamp, D.A., Seasonal Patterns of Predation on Juvenile Pacific Salmon by Anadromous Cutthroat Trout in Puget Sound. Transactions of the American Fisheries Society, 137(1), pp Eggleston, D.B. et al., Estuarine fronts as conduits for larval transport: hydrodynamics and spatial distribution of Dungeness crab postlarvae. Marine Ecology-Progress Series, 164, pp Folmar, L.C. & Dickhoff, W.W., The parr-smolt transformation (smoltification) and seawater adaptation in salmonids. Aquaculture, 21, pp Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 73

78 Fresh, K. et al., Role of the estuary in the recovery of Columbia River basin salmon and steelhead: An evaluation of the effects of selected factors on salmonid population viability., p.125. Fresh, K.L. et al., Juvenile Salmon use of Sinclair Inlet, Washington in 2001 and Washington Department of Fish and Wildlife, (March). Gonor, J.J., Sedell, J.R. & Benner, P.A., What we know about large trees in estuaries, in the sea, and on coastal beaches. In C. Maser et al., eds. From the forest to the sea: a story of fallen trees. Portland, OR: U.S. Forest Service, Pacific Northwest Research Station, pp Greene, C.M. et al., Improved viability of populations with diverse life-history portfolios. Biology Letters, 6(3), pp Gregory, R.S. & Levings, C.D., Turbidity reduces predation on migrating juvenile Pacific salmon. Transactions of the American Fisheries Society, 127(2), pp Healey, M.C., Utilization of the Nanaimo River estuary by juvenile Chinook salmon, Oncorhynchus tshawystcha. Fishery Bulletin, 79(3), pp Henning, J.A., Gresswell, R.E. & Fleming, I. a., Use of seasonal freshwater wetlands by fishes in a temperate river floodplain. Journal of Fish Biology, 71(2), pp Henning, J.A., Gresswell, R.E. & Fleming, I.A., Juvenile Salmonid Use of Freshwater Emergent Wetlands in the Floodplain and Its Implications for Conservation Management. North American Journal of Fisheries Management, 26(2), pp Hering, D.K. et al., Tidal movements and residency of subyearling Chinook salmon (Oncorhynchus tshawytscha) in an Oregon salt marsh channel. Canadian Journal of Fisheries and Aquatic Sciences, 67(3), pp Hiss, J., Meyer, J. & Boomer, R., Status of Chehalis River salmon and steelhead fisheries and problems affecting the Chehalis Tribe., p.61. Iwata, M. & Komatsu, S., Importance of estuarine residence for adaptation of chum salmon (Oncorhynchus keta ) fry to seawater. Canadian Journal of Fisheries and Aquatic Sciences, 41(5), pp Jeanes, E.D. & Morello, C.M., Native char utilization: Lower Chehalis River and Grays Harbor Estuary, Aberdeen, Washington., p.81. Koski, K. V, The Fate of Coho Salmon Nomads : The Story of an Estuarine-Rearing. Ecology And Society, 14(1). Levy, D.A. & Northcote, T.G., Juvenile salmon residency in a marsh area of the Fraser River estuary. Canadian Journal of Fisheries and Aquatic Sciences, 39(2), pp Maier, G.O. & Simenstad, C.A., The Role of Marsh-Derived Macrodetritus to the Food Webs of Juvenile Chinook Salmon in a Large Altered Estuary. Estuaries and Coasts, 32(5), pp Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 74

79 Mayama, H. & Ishida, Y., Japanese studies on the early ocean life of juvenile salmon, McCune, B. & Grace, J.B., Analysis of ecological communities, Gleneden Beach, Oregon: MJM Software Design. Moser, M.L., Olson, A.F. & Quinn, T.P., Riverine and estuarine migratory behavior of coho salmon (Oncorhynchus kisutch) smolts. Canadian Journal of Fisheries and Aquatic Sciences, 48(9), pp Mullahy, J., Specification and testing of some modified count data models. Journal of Econometrics, 33(3), pp Myers, J.M. et al., Status review of Chinook salmon from Washington, Idaho, Oregon, and California, NMFS, NOAA Technical memorandum 25. Naiman, R.J. & Sibert, J.R., Detritus and juvenile salmon production in the Nanaimo Estuary. III. Importance of detrital carbon to the estuarine ecosystem. Journal of the Fisheries Research Board, Canada, 36, pp Nelder, J.A. & Wedderbu, R.W., Generalized Linear Models. Journal of the Royal Statistical Society, Series A-General, 135(3), pp Quinn, T.P., The behavior and ecology of Pacific salmon and trout, Bethesda, Maryland: American Fisheries Society and the University of Washington Press. R Team, R.D.., R: A language and environment for statistical computing. Ralph, S.C., Peterson, N.P. & Mendoza, C.C., An inventory of off-channel habitat of the lower Chehalis River with applications of remote sensing. De Robertis, A. et al., Differential effects of turbidity on prey consumption of piscivorous and planktivorous fish. Canadian Journal of Fisheries and Aquatic Sciences, 60(12), pp Schroder, S. & Fresh, K., Results of the Grays Harbor coho survival investigations, , p.413. Seeb, L.W. et al., Development of a standardized DNA database for Chinook salmon. Fisheries, 32(11), pp Simenstad, C.A. et al., Ecological status of a created estuarine slough in the Chehalis River estuary: report of monitoring in created and natural estuarine sloughs. Simenstad, C.A. & Eggers, D.M., Juvenile salmonid and baitfish distribution, abundance, and prey resources in selected areas of Grays Harbor, Washington, Seattle. Simenstad, C.A., Fresh, K.L. & Salo, E.O., The role of Puget Sound and Washington coastal estuaries in the life history of Pacific salmon: An unappreciated function. In V. S. Kennedy, ed. Estuarine Comparisons. New York: Academic Press, pp Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 75

80 Smith, C.J. & Wenger, M., Salmon and Steelhead habitat limiting factors: Chehalis basin and nearby drainages, WRIA 22 and 23., p.448. Sommer, T.R. et al., Floodplain rearing of juvenile chinook salmon: evidence of enhanced growth and survival. Canadian Journal of Fisheries and Aquatic Sciences, 58(2), pp Swales, S. & Levings, C.D., Role of off-channel ponds in the life-cycle of coho salmon (Oncorhynchuskisutch) and other juvenile salmonids in the Coldwater River, British Columbia. Canadian Journal of Fisheries and Aquatic Sciences, 46(2), pp Team, W.E., A Comparative Assessment of a Natural and Created Estuarine Slough as Rearing Habitat for Juvenile Chinook and Coho Salmon. Estuaries, (4), pp Thorpe, J.E., Salmonid fishes and the estuarine environment. Estuaries, 17(1A), pp Tokar, E.M., Tollefson, R. & Denison, J.G., Grays Harbor: downstream migrant salmonid study., p.93. Tschaplinski, P.J., The use of esturies as rearing habitats by juvenile coho salmon. In T. W. Chamberlin, ed. Applying 15 years of Carnation Creek Results. Nanaimo, B.C.: Pacific Biological Station, pp USDA, NAIP Aerial Imagery., 2011(January). USFWS, Classification of Wetlands and Deepwater Habitats of the United States., 2011(January). WADNR, Washington State shorezone inventory., 2011(January). Wick, A.J., Ecological function and spatial dynamics of large woody debris in oligohaline brackish estuarine sloughs for juvenile Pacific salmon. School of Aquatic and Fisheries Sciences, p.125. Wissmar, R.C. & Simenstad, C.A., Energetic Constraints of Juvenile Chum Salmon (Oncorhynchus keta) Migrating in Estuaries. Canadian Journal of Fisheries and Aquatic Sciences, 45, pp Wood, B. & Stark, J.D., Acute toxicity of drainage ditch water from a Washington state cranberrygrowing region to Daphnia pulex in laboratory bioassays. Ecotoxicology and Environmental Safety, 53(2), pp Wright, S.G., Resident and anadromous fishes of the Chehalis and Satsop Rivers in the vicinity of Washington public power supply system s proposed nuclear project no.3., p.26. Zaugg, W.S., Prentice, E.F. & Waknitz, F.W., Importance of river migration to the development of seawater tolerance in Columbia River anadromous salmonids. Aquaculture, 51(1), pp Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 76

81 Appendices Appendix 1: Core and secondary sites sampled, Site name Latitude Longitude Site type Charlie Creek core site X X Chehalis River near restoration site core site X X X Chenois Creek flats core site X X X Cow Point core site X X X Damon Point core site X X X East Fork Hoquiam River core site X X X Elk River flats (South Bay forest) core site X X X Goose Island flats (NW corner) core site X X X Humptulips River right channel core site X X X Humptulips River mouth core site X X X Johns River channel core site X X X Lower Elliot Slough core site X X X Moon Island core site X X X Rennie Island core site X X Sand Island channel (North side) core site X X X Sand Island east alt. (mud beach) core site X X Sculpin Cove (upper Elk River) core site X X X Stearn's Bluff core site X X X West Fork Hoquiam River core site X X X Westport Marina (South Bay channel) core site X X X Wynoochee River delta core site X X X Beardslee Slough new secondary site X Chinook eddy secondary site X X Half Moon Bay (Westport) secondary site X X X Hoquiam mainstem secondary site X X Little Hoquiam River secondary site X Mallard Slough secondary site X X West Fork Hoqiuam River mouth secondary site X Withcomb Flats (North side) secondary site X X X Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 77

82 Appendix 2: Salmon density by habitat type, Chinook salmon density by habitat type, 2012 Coho salmon density by habitat type, 2012 Chum salmon density by habitat type, 2012 Cutthroat trout density by habitat type, 2012 Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 78

83 Chinook salmon density by habitat type, 2011 Coho salmon density by habitat type, 2011 Chum salmon density by habitat type, 2011 Cutthroat trout density by habitat type, 2011 Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 79

84 Appendix 3: Juvenile Salmon Density and Distribution Plots, Unmarked YOY Chinook salmon No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 80

85 Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 81

86 No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 82

87 Hatchery YOY Chinook salmon (empty panels indicate low or no catch in those months) No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 83

88 Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 84

89 No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 85

90 Unmarked YOY coho salmon (missing panels indicate low or no catch in those months) No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 86

91 Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 87

92 No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 88

93 Unmarked yearling coho salmon (missing panels indicate low or no catch in those months) No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 89

94 Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 90

95 No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 91

96 Hatchery yearling coho salmon (missing panels indicate low or no catch in those months) No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 92

97 Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 93

98 No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 94

99 YOY chum salmon (all are unmarked; missing panels indicate low or no catch in those months) No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 95

100 Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 96

101 No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 97

102 Appendix 4: Juvenile Dungeness Crab Density and Distribution Plots, No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 98

103 Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 99

104 No sampling in February Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 100

105 Appendix 5: Online resources for estimating tidal heights Site name Zone Tide predictor Website Half Moon Bay [aka Westport ocean side] Mouth Westport Westport Marina (South Bay Channel) South Bay Westport Elk River Flats (aka South Bay Forest) South Bay Bay City Beardslee Slough South Bay Bay City Beardslee Slough Mouth South Bay Bay City Mallard Slough South Bay Bay City John's River channel South Bay Markham John's River slough South Bay Markham Ocean Shores Flats 1 North Bay Westport North Bay Flats 1 (aka Humptulips flats 1) North Bay Westport North Bay Flats 2 (aka Humptulips flats 2) North Bay Westport Campbell Slough North Bay Westport Humptulips River mouth North Bay Westport Jessie Slough North Bay Westport Chinois Creek Flats Alternate North Bay Westport Chinois Creek Flats Alternate 2 North Bay Westport Chinois Creek Flats 1 North Bay Westport Chinois Creek Flats 2 North Bay Westport Sand Island channel (North side) Central estuary Westport Sand Island Flats (South side) Central estuary Westport Goose Island Flats (NW corner) Central estuary Westport North Bay Bar (Goose Island Alt.) Central estuary Westport Damon Point Central estuary Westport Bar off John's River Central estuary Markham Withcomb Flats Central estuary Westport Stearn's Bluff Central estuary Markham Moon Island Upper estuary Aberdeen Cow Point Upper estuary Aberdeen West Fork Hoquiam River Upper estuary Aberdeen West Fork Hoquiam River Mouth Upper estuary Aberdeen Hoquiam River Upper estuary Aberdeen Hoquiam River slough Upper estuary Aberdeen East Fork Hoquiam River Upper estuary Aberdeen Wishkah River Channel Upper estuary Aberdeen Wishkah River Slough Upper estuary Aberdeen Lower Elliot Slough Surge Plain Cosmopolis Preacher's Slough (corner) Surge Plain Cosmopolis Sand Island East Surge Plain Cosmopolis Preacher Slough Restoration Surge Plain Cosmopolis Wynoochee River Surge Plain Cosmopolis Chehalis near Friends landing Surge Plain Cosmopolis Chehalis restoration site Surge Plain Cosmopolis Chehalis River surge plain Surge Plain Cosmopolis Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 101

106 Appendix 6: Stream flow on the Chehalis River at Porter, WA, A) B) Chehalis River discharge at Porter (USGS ) for: (A) 2013, (B) 2012, and (C) C) Grays Harbor Juvenile Fish Use Assessment, 2013 Wild Fish Conservancy Page 102