Fish Distribution and Periodicity in WRIA 1

Final Draft Fish Distribution and Periodicity in WRIA 1 Prepared for: City of Bellingham, Public Works Department 2221 Pacific Street Bellingham, WA 98226 Prepared by: Anchor Environmental, L.L.C. 1411 4 th Avenue, Suite 1210 Seattle, WA 98101 March 2001

Table of Contents 1 Introduction... 4 2 Anadromous Salmonids of WRIA 1... 6 2.1 Life Histories... 7 2.1.1 Chinook Salmon... 7 2.1.2 Coho Salmon... 8 2.1.3 Chum Salmon... 9 2.1.4 Pink Salmon... 10 2.1.5 Sockeye Salmon... 10 2.1.6 Steelhead Trout... 11 2.1.7 Bull Trout/Dolly Varden... 12 2.1.8 Coastal Cutthroat Trout... 13 2.2 Periodicity... 15 3 Native Non-Anadromous Salmonids of WRIA 1... 17 3.1 Bull Trout / Dolly Varden... 17 3.1.1 Life History... 17 3.1.2 Distribution... 17 3.1.3 Periodicity... 17 3.2 Coastal Cutthroat Trout... 18 3.2.1 Distribution... 18 3.2.2 Periodicity... 19 3.3 Kokanee... 19 3.3.1 Life History and Habitats... 19 3.3.2 Distribution... 20 3.3.3 Periodicity... 20 3.4 Rainbow Trout... 20 3.4.1 Life History and Habitats... 20 3.4.2 Distribution... 21 3.4.3 Periodicity... 21 4 Non-native Non-anadromous salmonids in WRIA 1... 22 4.1 Eastern Brook Trout... 22 4.2 Brown trout... 22 5 Native Non-Salmonids in WRIA 1... 22 5.1 Lamprey... 22 5.1.1 Life History and Habitats... 22 5.1.2 Distribution... 23 5.1.3 Periodicity... 24

5.2 Sturgeon... 24 5.2.1 Life History and Habitats... 24 5.2.2 Distribution... 25 5.2.3 Periodicity... 25 5.3 Mountain Whitefish... 25 5.3.1 Life History and Habitats... 25 5.3.2 Distribution... 26 5.3.3 Periodicity... 26 5.4 Longfin Smelt... 26 5.4.1 Life History and Habitats... 26 5.4.2 Distribution... 27 5.4.3 Periodicity... 27 5.5 Dace... 27 5.5.1 Life History and Habitats... 27 5.5.2 Distribution... 28 5.5.3 Periodicity... 28 5.6 Suckers... 28 5.6.1 Life History and Habitats... 29 5.6.2 Distribution... 29 5.6.3 Periodicity... 29 5.7 Sculpin, Sticklebacks, and Peamouth... 30 6 Non-Native Non-Salmonids in WRIA 1... 32 7 Other Species of Record... 32 8 References... 33

1 INTRODUCTION This report summarizes the life history, distribution, and periodicity of fishes occurring in Washington State Water Resources Inventory Area 1 (WRIA 1). WRIA 1 includes the Nooksack River Basin, independent drainages that flow directly to the estuary, and partial watersheds of two river systems that flow north to the Fraser River system in Canada. This information was compiled through a review of literature specific to WRIA 1 areas, general literature, input from the WRIA 1 Instream Flow/Fish Habitat Technical Team (Technical Team), interviews with area biologists, the Salmon and Steelhead Inventory Assessment Project (SSHIAP) database, and Washington Department of Fish and Wildlife (WDFW) databases and distribution maps. Distribution and periodicity information for most of the non-salmonid species in WRIA 1 is very limited, particularly in drainages other than the Nooksack River. Sources such as Wydoski and Whitney (1979) and McPhail and Lindsey (1970) provide general species information on habitats and life history used to project those parts of the river systems where the given fish species may occur and the timing of their movements and spawning activities. For current information on the distribution of anadromous salmonids in WRIA 1, please refer to the database compiled by SSHIAP (2000). The collaborative SSHIAP effort created a database that documents the distribution observations provided by the area s fish biologists. Distribution maps were created in ArcView GIS for four Pacific salmon species, as well as native char and trout. It is important to note that the maps document where fish are known to exist, but do not depict the absence of fish. That is, several areas in WRIA 1 have not been surveyed and therefore these fish communities are not known (Hyatt 2000). The database documents distribution points in WRIA 1, including the species or stock(s) that reach that point, whether the fish presence is known or presumed, whether a known barrier is passable or impassable, whether spawning was noted at the site, the source(s) of information used for the observation, and the biologist(s) making the observation. WDFW also maintains a separate bull trout/dolly Varden distribution map and database that continues to be updated. This report does not investigate stock origins (i.e., hatchery vs. wild) which may be pertinent to the decision-making and prioritization necessary for the ultimate goal of preparing a Watershed Management Plan for WRIA 1. The influence of hatchery plantings Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 4

on salmonid gene pools in WRIA 1 is a useful topic for additional research. The Lummi Nation, Nooksack Tribe, and WDFW are collaborating on an investigation of the genetic makeup of chinook and coho salmon spawning in the Nooksack River system. Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 5

2 ANADROMOUS SALMONIDS OF WRIA 1 The anadromous salmonid fish community of WRIA 1 includes all five Pacific salmon species, steelhead trout, coastal cutthroat trout, bull trout, and Dolly Varden. All of these species are native to WRIA 1. Currently, two salmonid species in the WRIA 1, chinook salmon and bull trout, are federally listed as threatened under the Endangered Species Act (ESA). Coho salmon in the area are a candidate for listing under ESA. An overview of the WRIA 1 anadromous salmonid stock information compiled in the Salmon and Steelhead Stock Inventory (SASSI; WDF et al. 1993) and subsequent appendices (WDFW 1998; WDFW 2000a) is presented in Table 1. Table 1. Status of Anadromous Salmonid Stocks in WRIA 1. Species Stock Origin Production Status Chinook Spring North Fork Nooksack Native Composite Critical Chinook Spring South Fork Nooksack Native Wild Critical Chinook Fall Samish/ Mainstem Nooksack Non-native Composite Unknown Chinook a Fall Whatcom Creek Non-native Composite Unknown Coho Nooksack Mixed Composite Unknown Coho North Puget Sound Tributaries Mixed Wild Unknown Coho a Whatcom Creek Mixed Wild Unknown Coho Sumas/ Chilliwack Native Wild Unknown Chum Fall North Fork Nooksack Native Wild Healthy Chum Fall Mainstem/ South Fork Nooksack Native Wild Unknown Chum Fall Independent Drainages Mixed Composite Healthy Chum a Fall Whatcom Creek Mixed Composite Unknown Chum Fall Sumas/ Chilliwack Native Wild Unknown Pink North Fork/ Middle Fork Nooksack Mixed Wild Unknown Pink South Fork Nooksack Native Wild Unknown Sockeye b Nooksack Native Wild Unknown Steelhead Summer South Fork Nooksack Native Wild Unknown Steelhead Winter Mainstem/ North Fork Nooksack Native Wild Unknown Steelhead Winter South Fork Nooksack Native Wild Unknown Steelhead Winter Middle Fork Nooksack Native Wild C Unknown Steelhead a Winter Whatcom Creek Native Wild Unknown Steelhead Winter Dakota Creek Native Wild Unknown Bull Trout/ Dolly Varden Lower Nooksack Native Wild Unknown Bull Trout/ Dolly Varden Upper Middle Fork Nooksack Native Wild Unknown Bull Trout/ Dolly Varden Canyon Creek (North Fork Nooksack Trib.) Native Wild Unknown Bull Trout/ Dolly Varden Chilliwack/ Selesia Creek Native Wild Unknown Coastal Cutthroat Nooksack Mixed Composite Unknown Coastal Cutthroat Whatcom Creek Native Wild Unknown Coastal Cutthroat Sumas Native Wild Unknown Coastal Cutthroat North Puget Sound Tributaries Native Wild Unknown Notes: (a) Chinook, chum, coho, and steelhead stocks in Whatcom Creek are not defined in SASSI, although they are known to occur there. Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 6

(b) Riverine sockeye salmon occur in the Nooksack River, but the stock was not defined in SASSI. (c) The Middle Fork Nooksack steelhead stock has been supplemented with hatchery fish since the SASSI report. 2.1 Life Histories 2.1.1 Chinook Salmon The Puget Sound chinook salmon (Oncorhynchus tshawytscha) evolutionarily significant unit (ESU) is listed as a threatened species under ESA. This ESU includes all naturally spawned populations of chinook salmon from rivers and streams flowing into Puget Sound and the Northwest Straits. Critical habitat including all marine, estuarine, and river reaches accessible to chinook salmon in Puget Sound is also protected. Two races of chinook salmon return to the Nooksack River: spring-run and fall-run fish. A fall-run of chinook salmon returns each year to Whatcom Creek. Race name is based on the timing of adult entry into the freshwater system. The spring-run is native and has both wild and hatchery production. The North Fork spring-run is supplemented by hatchery operations at the Kendall hatchery, whose operations are considered essential for recovery of the stock (NOAA 1999). The Nooksack River fall-run is primarily a non-native composite stock originating from fall chinook salmon in the Green River. At one time, a distinct wild summer-run returned to the river; however, hatchery and harvest management practices and habitat degradation have essentially eliminated the run (CES et al. 1994). Both races of chinook salmon exhibit ocean-type and stream-type life history strategies. Ocean-type chinook salmon leave the river environment and enter the estuarine and marine environment during their first year of life, typically within three to four months after emergence (Healey 1991). Ocean-type chinook salmon generally spend most of their marine migrations in coastal waters and return to their natal river in the fall, a few days or weeks before spawning. Ocean-type chinook salmon tend to depend heavily on estuaries for juvenile rearing, more so than stream-type chinook salmon and the other species of salmon (Simenstad et al. 1982). Stream-type chinook salmon spend one or more years in freshwater before migrating to sea and undertake extensive offshore migrations. Stream-type chinook salmon return to their natal river in the spring or summer, often several months prior to spawning. Stream-type chinook salmon is the most sensitive life history Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 7

form due to their long holding period in the mainstem during summer low-flow conditions (Fox 1994). Ocean-type chinook salmon is the predominant life history form found south of 56 o N latitude, i.e., in the continental United States (Healey 1991). In the Nooksack River, approximately 95% of the North Fork spring chinook salmon have oceantype life histories (Currence 2000). However, in the South Fork Nooksack, the majority of spring chinook salmon (estimated 55% to 67%) exhibit stream-type life histories. No such information is available for the Middle Fork, although they are generally considered more closely related to the North Fork stock. Juveniles from the mainstem spawning areas are primarily ocean-type (Currence 2000). Chinook salmon typically stay in marine waters for three or four years (range one to eight) before returning to their natal rivers to spawn (Beauchamp et al. 1983). Spawning occurs in all three forks of the Nooksack River, as well as the mainstem. Chinook salmon are generally considered main channel spawners, although they will use smaller channels and streams with sufficient flow. Due to their large size, chinook salmon are able to spawn in larger substrate (up to 14 cm) that most other salmon species. Chinook salmon spawning locations are typically 24 cm deep, with velocities between 30 and 91 cm/s and substrate between 1.3 and 10.2 cm (Thompson 1972; Bell 1986). As for all salmonid species, the duration of egg development before hatching is related to temperature; eggs develop slower in cooler temperatures and survival is limited above 16 C. An estimate of time to hatching can be estimated by a simple thermal model: development time = 468.7/T, where T is the average Celsius temperature during incubation. Eggs often incubate more than 100 days prior to hatching. The alevins remain in the gravel for four to six weeks until the yolk sac is absorbed (Beauchamp et al. 1983). Juvenile chinook salmon in freshwater occupy areas of increasing depth and velocity as they increase in size (Chapman and Bjornn 1968). 2.1.2 Coho Salmon The Puget Sound/Strait of Georgia coho salmon (O. kisutch) ESU is currently a candidate species for ESA listing by NMFS. The ESU includes all naturally spawned populations of coho salmon from rivers and streams flowing into Puget Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 8

Sound. Along with chum, coho salmon are distributed among the widest range of river and tributary systems in WRIA 1. Coho salmon typically remain in the marine environment for up to 18 months before returning to their natal streams to spawn (Sandercock 1991). A subset of males called jacks return after only five to seven months at sea. Coho salmon spawn in small tributary streams, as well all three forks and mainstem Nooksack River. Coho salmon spawning locations are typically 18 cm deep, with velocities between 30 and 91 cm/s and substrate between 1.3 and 10.2 cm (Thompson 1972; Bjornn and Reiser 1991). Juvenile coho salmon rear in freshwater for approximately one year, and go to sea in the spring of their second year. Juvenile coho salmon in freshwater are territorial and actively defend feeding territories. Low velocity pools and riffles in tributary streams and quiet water areas such as sloughs, wetland, and side channels are important rearing and overwintering areas for juvenile coho salmon (CES et al. 1994). As they migrate into the marine environment, juvenile coho salmon tend to use the shallow nearshore habitats less than other salmon species (Simenstad 1983). Coho salmon typically undergo ocean migrations across the North Pacific Ocean; however, up to 5 percent of the naturally produced yearling coho salmon entering Puget Sound may remain inside the Strait of Juan de Fuca until maturity without migrating to the Pacific Ocean (Simenstad et al. 1982). 2.1.3 Chum Salmon Chum salmon (O. keta) typically remain in the marine environment for two to five years before returning to their natal streams to spawn (Salo 1991). Chum salmon are large, strong swimmers capable of swimming in high velocity currents. They are not good leapers and are typically only found below the first barrier of any significance in a river. In the Nooksack River, most chum salmon spawning occurs above river kilometer (RKm) 56 in the North, Middle, and South Forks with limited spawning documented in the mainstem (CES et al. 1994). In general, chum salmon spawn in shallower, slower-running waters with side channels more than do other salmonid species, perhaps to avoid competition with pink salmon (Salo 1991). Water velocities at chum salmon spawning locations often range between 21.3 and 83.8 cm/sec (Johnson et al. 1971). Chum salmon spawning locations are typically 18 cm deep, with substrate between 1.3 and 10.2 cm (Thompson 1972; Bell 1986). Generally, juvenile chum salmon do not rear for an extended period of time in Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 9

freshwater. In spawning ground areas close to saltwater, chum salmon outmigration may occur the first night after emergence (CES et al. 1994). However, juvenile chum salmon between 50 and 65 mm in length are regularly captured in the Lummi Nation s rotary screwtrap on the mainstem Nooksack River at RKm 9.6 (MacKay 2000). These sizes suggest weeks of freshwater rearing in freshwater by some chum prior to migrating to sea. 2.1.4 Pink Salmon The pink salmon (O. gorbuscha) life cycle has the least variability of the Pacific salmon species. With few exceptions, pink salmon in WRIA 1 return to spawn only on the odd-numbered years. Upon emergence, pink salmon migrate quickly to sea and grow rapidly as they make extensive feeding migrations (Heard 1991). After 18 months in the marine environment they return to their natal streams to spawn. This species tends to spawn closer to tidewater than other species of Pacific salmon, generally within 50 km of a river mouth (Heard 1991, WDF et al. 1993). In the Nooksack River, the migrations of most pink salmon are longer, as pink salmon spawn in nearly every accessible tributary in the three forks of the Nooksack River (Fox 1994). Some additional spawning occurs in side channels of the mainstem Nooksack River. Pink salmon prefer to spawn in shallow pools and riffles with clean, coarse gravel and moderately fast currents. Pink salmon spawning locations are typically 15 cm deep, with velocities between 21 and 101 cm/s and substrate between 1.3 and 10.2 cm (Thompson 1972; Bell 1986). Bell (1986) identified water temperatures between 7.2 C and 12.8 C as recommended for pink salmon spawning. Pink salmon spawn in a wide range of temperatures, but spawning activity tends to drop off sharply above 16 C. Upon emerging from the gravel, pink salmon alevins migrate rapidly downstream, generally in schools and usually in darkness. 2.1.5 Sockeye Salmon Riverine populations of sockeye salmon (O. nerka) occur in the Nooksack River, although little information is known about them and a sockeye salmon stock in WRIA 1 was not documented in SASSI (WDF et al. 1993). Small runs of native sockeye salmon spawn in the North and South Forks (Hendrick 1993 as cited in Fox 1994). Sockeye salmon typically spend between one and four years in the marine Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 10

environment before returning to their natal streams to spawn. Sockeye salmon spawning locations are typically 15 cm deep, with velocities between 21 and 101 cm/s and substrate between 1.3 and 10.2 cm (Bell 1986; Bjornn and Reiser 1991). Sockeye salmon in the Nooksack River are riverine and do not have access to rearing lakes typically associated with the species. Instead, juveniles spend one or two years rearing in off-channel, low velocity river habitats prior to migrating to sea (Gustafson and Winans 1999). 2.1.6 Steelhead Trout Two races of steelhead trout (O. mykiss) return to the Nooksack River: summer-run and winter-run fish. Winter-run steelhead trout also return to Whatcom and Dakota Creeks. Winter-run steelhead trout are augmented by a hatchery stock that has a different migration and spawning timetable (Fox 1994). Rainbow trout are the non-anadromous form of steelhead trout. A small component of the steelhead trout run residualize and stay in freshwater, thus contributing resident rainbow trout populations. The steelhead trout races are named based on the timing of adult entry into the freshwater system. Winter-run steelhead trout enter their natal river in the fall and winter in various stages of maturation and spawn within the next few months after entering the river (Pauley et al. 1986). Summer-run steelhead trout enter their natal river during the spring and summer as immature fish and do not mature and spawn until the following spring. Summer-run steelhead trout adults migrate upstream and hold in deep pools until river levels rise during autumn rains to allow upstream passage to spawning areas (Fox 1994). Summer-run steelhead trout are effectively isolated from winter-run steelhead trout because they are more successful at passing intermittent barriers (Johnston 1993 as cited in Fox 1994). Unlike the Pacific salmon species, steelhead trout are iteroparous, that is they do not invariably die after spawning. Although significant post-spawning mortality occurs, a small number of steelhead trout adults migrate out of the river after spawning and return to spawn in subsequent years (Busby et al. 1996). Steelhead trout exhibit a great diversity in life history patterns as individuals rear in freshwater between one and four years and remain at between one and four years (Meehan and Bjornn 1991). Steelhead trout spawning locations are typically 24 Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 11

cm deep with velocities between 40 and 91 cm/s and substrate between 0.6 and 10.2 cm (Smith 1973; Hunter 1973). Steelhead trout eggs usually hatch in four to seven weeks and alevins emerge from the gravel in three to seven days (Pauley et al. 1986). After emergence, young steelhead trout often compete with young coho salmon, chinook salmon, cutthroat trout, bull trout, and Dolly Varden for food and space (Meehan and Bjornn 1991). As the fish grow they are able to move into deeper parts of the stream and establish feeding territories. 2.1.7 Bull Trout/Dolly Varden Bull trout (Salvelinus confluentus) and Dolly Varden (S. malma) are the only char in the family Salmonidae that are native to Washington. Bull trout were originally classified with Dolly Varden) under one scientific name, but in 1991 the American Fisheries Society supported the decision to split them into two distinct species. Information on the distribution and life history of each species is not yet distinct because the species are biologically similar and methods to separate them are new and not widely applied (Bonar 1997). Given the lack of distinct information for the species, this discussion will group the species together. There are reports that bull trout/dolly Varden in the Nooksack River system have spawned with the introduced eastern brook trout (S. fontinalis) to produce hybrids (Huddle 2001; Hendrick 2001; Johnston 2001a). Bull trout/dolly Varden exhibit four life history strategies. Three of these strategies are carried out entirely in freshwater and are discussed in Section 3. The fourth form are anadromous bull trout whose life history includes migrations to and from saltwater where abundant food resources result in this fish becoming larger (up to 900 mm) than other life history forms (Johnston 1996). The anadromous life history form of bull trout/dolly Varden is more complex than the freshwater forms (Johnston 1996). Smolts outmigrate to the river mouth and nearshore areas where they feed and grow rapidly during the spring and summer. In late summer and early fall these sub-adults move from the marine environment to the lower river reaches and tributaries. These migrations often include movements into river systems other than their natal streams. After overwintering in freshwater, sub-adults return to the marine environment. Bull trout become Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 12

sexually mature at 5 to 7 years of age and can live up to 20 years (Rieman and McIntyre 1993). Bull trout/dolly Varden require cold, clean water and prefer water temperatures below 13 C (WDFW 1999). Although their distribution is strongly influenced by water temperature (Rieman and McIntyre 1993; Bonneau and Scarnechia 1996; Lee et al. 1997), the migrations of the anadromous form includes movement into water as high as 24 C (Kraemer in prep. as cited in Johnston 1996). This indicates they are fairly temperature tolerant during those life stages. Spawning occurs in the upriver tributaries when stream temperatures decrease below 9 C or 10 C (McPhail and Murray 1979; Fraley and Shepard 1989). Egg survival requires extremely cold water, optimally 2 C to 4 C (Johnston 1996). In many cases, anadromous, fluvial, and resident adults spawn in the same areas (WDFW 1998) and adults are repeat spawners over multiple years. Bull trout/dolly Varden spawn on gravel and cobble substrate (Baxter and McPhail 1996). Adults leave the spawning area soon after spawning (Johnston 1996). Post-spawn bull trout/dolly Varden are often found holding in the lower halves of pools or runs with 1 to 2 m of water. After emerging from the gravel, young fry remain in close proximity to large substrate such as cobble, boulders, and large organic debris like root wads (Johnston 1996). Juveniles found near larger rocks would often seek cover in the substrate during daylight hours and emerge during periods of darkness. Bull trout/dolly Varden juveniles typically remain in their natal stream until age-2 before migrating downstream. 2.1.8 Coastal Cutthroat Trout Coastal cutthroat trout (O. clarki clarki) in WRIA 1 are a native species, however their distribution in WRIA 1 has been expanded through hatchery plantings (Johnston 2001a). Like bull trout/dolly Varden, coastal cutthroat trout exhibit four general life history forms, including an anadromous form. All coastal cutthroat trout populations with access to the sea are believed to have an anadromous component (Giger 1972, Sumner 1972, Trotter 1989). The life history of coastal cutthroat trout is perhaps the most complex of the Pacific salmonids (Northcote 1997). Most coastal cutthroat trout that do enter seawater do Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 13

so as 2- or 3-year-olds, but some remain in freshwater for up to six years before entering the sea (Giger 1972, Sumner 1972). After feeding in salt water and estuaries for several months, most coastal cutthroat trout return to freshwater to overwinter and spawn (WDFW 2000a). Coastal cutthroat trout are iteroparous, and the incidence of repeat spawning appears to be higher than in steelhead trout (Giger 1972, Busby et al. 1996). Coastal cutthroat trout have been documented to spawn each year for at least 5 years (Giger 1972), although some do not spawn every year (Tomasson 1978). Some coastal cutthroat trout do not return to seawater after spawning but instead remain in freshwater for at least a year (Giger 1972, Tomasson 1978). Second-time and third-time spawning females produce more eggs and larger eggs than first-time spawning females (WDFW 2000a). Coastal cutthroat trout generally spawn upstream of coho salmon and steelhead trout spawning zones, although some overlap may occur (Lowry 1965, Edie 1975, Johnston 1982). Spawning typically occurs in riffles where water depths are between 15 and 45 cm with low gradient and low flow (Johnston 1982; Trotter 1989). Redds are constructed on pea-size gravel, usually near pools (Hunter 1973; Jones 1978). Redds are primarily built in the tails of pools in streams with low stream gradient and low flows, usually less than 0.3 m 3 /s during the summer (Johnston 1982). Eggs begin to hatch within 6 to 7 weeks of spawning, depending on temperature, and alevins remain in the gravel for about two weeks after hatching (Giger 1972, Scott and Crossman 1973; Trotter 1989). At emergence, fry quickly migrate to channel margins and backwaters, where they remain throughout the summer (Glova and Mason 1976, Moore and Gregory 1988). There is some disagreement in the literature regarding the preferred habitat type of fry. When they are the only salmonid in the stream, age-0 coastal cutthroat trout are more abundant in pools, but use riffles and glides as well (Glova 1984). In contrast, in sympatry with coho salmon fry and sculpins, coastal cutthroat trout are fairly evenly distributed between all three habitat types (Glova 1978, 1987). The reduced use of pools while in sympatry has been interpreted as evidence that coastal cutthroat trout are relegated to riffles by socially dominant coho salmon (Glova 1978, 1984; Johnston 1982; Trotter 1997). Other authors have found that underyearling coastal cutthroat trout select the shallower and faster waters in riffles (June 1981, Bisson et al. 1982, Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 14

Bisson and Sedell 1984, Mitchell 1988) but may reduce their use of this habitat type in the presence of steelhead trout (Bisson et al. 1982). In winter, coastal cutthroat trout move to pools near log jams or overhanging banks (Bustard and Narver 1975). Coastal cutthroat trout generally remain in upper tributaries until they are one year of age, when they may begin moving more extensively throughout the river system (Johnson et al. 1999). Juvenile coastal cutthroat trout may migrate upriver and downriver within the system during different times of the year prior to their outmigration beyond the estuary (Johnson et al. 1999). Upstream movement of juveniles with parr marks from estuaries and mainstems to tributaries begins with the onset of winter freshets during November (Giger 1972; Cederholm and Scarlett 1982; Garrett 1998) and continued through the spring, frequently peaking during late winter and early spring (Cederholm and Scarlett 1982; Garrett 1998). 2.2 Periodicity The Technical Team developed preliminary anadromous salmonid periodicity charts using timing information reported in the literature as well as observations by Technical Team members and regional biologists (Table 2). The periodicity of each lifestage was defined conservatively. Consideration was given to actual observations as well as expected inner-annual variability and conditions when salmon stocks in the river are restored to higher numbers of fish. These charts represent a work in progress and will be revised by the Technical Team as more data become available. The following rules or assumptions were used in developing the periodicity charts: Periodicity was defined conservatively to ensure the entire timeframe for a lifestage is included. In this way, if a given lifestage occurs in the river during any part of the month, the entire month was included in the periodicity. Holding periodicity extends from the beginning of river entry to the end of spawning. Wild vs. hatchery stock periodicity is not differentiated. Bull trout and Dolly Varden periodicities are not differentiated because there is insufficient information to do so. Multiple versions of the anadromous salmonid periodicity charts have been prepared. Earlier versions presented in Tables 3, 4, and 5 are provided to document the changes in periodicity estimates and life stages delineated, as well as the sources Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 15

of input during the development of the charts. This information may be useful in future Technical Team efforts to refine the charts. Each version uses the most recent earlier version as its starting point. Table 3 was prepared in September 2000 and presents the periodicity information compiled from the literature. Sources for this literature-based periodicity included: Williams et al. 1975, WDF et al. 1993, CES et al. 1994, Fox 1994, Ecology 1995, USFS 1995, WDFW 1998, Conrad and MacKay 2000, WDFW 2000a, and WDFW 2000b. Table 4 provides the draft life stage periodicities developed at the WRIA 1 Habitat Suitability Criteria Workshop held in October 2000. At the workshop, some of the data sources used in the development of the literature-based were determined to be questionable, and revisions were made based on workshop participant input. Subsequent to the workshop, additional input was provided by Jim Johnston, the WDFW regional biologist. His comments are shown in Table 5. In addition to comments on anadromous trout periodicity, Johnston made the following recommendations: Distinguish between adult and juvenile outmigration timing Distinguish between hatchery and wild winter steelhead trout timing Provide peak timing periodicity information If a size is to be identified to differentiate fry and juvenile lifestages, use 70 mm The periodicity information presented here will be revised in the future as additional information from ongoing studies is obtained. The Technical Team intends to develop separate periodicities for different areas within WRIA 1 (e.g., independent drainages, Nooksack River lowland areas, and Nooksack River upper basin). In addition, the Technical Team plans to identify the typical or peak periodicities for the various species and life stages that occur in the river. Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 16

3 NATIVE NON-ANADROMOUS SALMONIDS OF WRIA 1 3.1 Bull Trout / Dolly Varden 3.1.1 Life History Three non-anadromous life history forms of bull trout/dolly Varden have been identified: fluvial, adfluvial, and resident. The fluvial form lives as an adult in large, mainstem rivers but spawns in small tributary streams, often the same ones used by the resident form (Johnston 1996). Adfluvial fish grow and mature in lakes or reservoirs, then move into tributary streams to spawn. The resident form spends its entire life in small headwater streams. Fluvial and adfluvial bull trout/dolly Varden usually reach sexual maturity in about their fifth year. All three forms can be long lived, often 10 to 15 years, allowing them to spawn in multiple years. The spawning, incubation, and rearing conditions as described for the anadromous form (Section 2) are applicable to the non-anadromous forms. 3.1.2 Distribution Bull trout/dolly Varden are distributed throughout the Nooksack River system. They occur throughout the anadromous zone and above barriers such as the falls on the South Fork at RKm 50 (WDFW 2001). Their distribution includes nearly the full extent of the Middle and South Forks of the Nooksack River. In the North Fork, bull trout/dolly Varden are not found above Nooksack Falls (RKm 105). Their distribution has been documented in several tributaries in the Nooksack River system. In the North Fork these include Racehorse, Maple, Boulder, Canyon, and Glacier Creeks. In the Middle Fork the longest runs are up Canyon Creek. In the South Fork, bull trout/dolly Varden are documented in Skookum and Howard Creeks. Non-anadromous bull trout/dolly Varden are not documented in the independent drainages, likely due to high water temperatures in those systems. 3.1.3 Periodicity Spawning migrations of freshwater bull trout/dolly Varden in the Skagit River occur as early as mid-august (Johnston 1996). Spawning occurs from September to November. Soon after spawning, fluvial and adfluvial adults leave the spawning area and migrate downstream. Fluvial adults move throughout the upper river Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 17

areas and remain in pools throughout the winter, spring, and early summer. Due to the cold water temperatures they spawn in, egg incubation extends to as long as 6 months. 3.2 Coastal Cutthroat Trout Like bull trout/dolly Varden, coastal cutthroat trout exhibit four general life history forms, including resident, fluvial, and adfluvial forms that remain in freshwater throughout their lives. Resident cutthroat trout are usually much smaller than the other life history forms and are typically smaller than 20 cm (8 in; WDFW 2000a). All life history forms move upstream to spawn in small streams (Trotter 1989) and their spawning areas often overlap. The non-anadromous coastal cutthroat trout forms require the same spawning, incubation, and rearing conditions as described for the anadromous form. 3.2.1 Distribution Coastal cutthroat trout are distributed throughout the Nooksack River system, occupying nearly every accessible stream (Fox 1994). Their distribution includes river reaches inaccessible to anadromous fish, include headwater areas of the North, Middle, and South Forks. Coastal cutthroat trout distributions in six North Fork and Middle Fork tributaries investigated was generally restricted to lower reaches as they were replaced by rainbow trout in the higher reaches of the streams (FERC 1994). Coastal cutthroat trout also occur in the independent drainages of WRIA 1, including an adfluvial population in Lake Terrell (WDFW 2000a). A genetically distinct population of adfluvial coastal cutthroat trout occurs in the Lake Whatcom watershed (WDFW 2000a). This population utilizes the lower reaches of tributary streams for spawning (Johnston 2001a). Adfluvial, resident, and anadromous coastal cutthroat trout also occur in Whatcom Creek (WDFW 2000a). Movement upstream from Whatcom Creek into Lake Whatcom is restricted by sluice gates operated by the City of Bellingham to maintain lake levels. However, downstream movement (of individuals from Lake Whatcom, likely contribute to the coastal cutthroat trout populations found in Whatcom Creek. Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 18

3.2.2 Periodicity The freshwater life history forms of coastal cutthroat trout undertake spawning, intragravel development, and early life history timing similar to the anadromous form. Spawning occurs from January to June in small streams (WDFW 2000a), except in the Lake Whatcom watershed where spawning concludes by the end of May (Johnston 1993). Post-spawned adults return to rivers or lakes soon after spawning. Eggs hatch within 30 to 45 days depending on temperature and alevins emerge from gravel between March and July (Scott and Crossman 1973; Johnston 2001a). Age-0 coastal cutthroat trout juveniles use pools, riffles, and glides depending on other salmon and trout species present. In the winter, juveniles move to pools near logjams or overhanging banks (Bustard and Narver 1975). Most juveniles remain in their natal streams, typically for one or two years prior to moving to the mainstem river (fluvial forms) or lake (adfluvial; Johnston 2001a). 3.3 Kokanee An endemic population of kokanee (O. nerka), the non-anadromous form of sockeye salmon, occurs in Lake Whatcom. These fish are land-locked and have been an isolated gene pool for an extended time, possibly since the last ice age approximately 10,000 years ago, with the exception of the introduction of at least one non-native planting in the early 1920 s (Looff 1994). Lake Whatcom kokanee are used as the brood stock for WDFW planting operations and has historically provided the largest source of eggs in the world. Lake Whatcom kokanee are currently the only source of kokanee eggs and fry throughout Washington (WDNR 1998). Wild kokanee populations in the Lake Whatcom watershed have declined significantly and most recent estimates are 500 or fewer spawners (Looff 1994; Johnston 2001b). Approximately 5 million kokanee fry are planted every year to Brannian Creek which flows into the south end of Lake Whatcom. 3.3.1 Life History and Habitats Kokanee spend most of their lives in lakes, moving throughout all areas and using depths between 0 and 30 m (Johnston 2001b). Kokanee typically spawn in tributary streams, but some spawning occurs at tributary outlets and along the lake edges (Wydoski and Whitney 1979). Kokanee spawn on cobble and gravel substrate, creating small, shallow redds. Kokanee typically spawn in locations less than 1 ft Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 19

deep with water velocities ranging from 0.4 to 3 ft/sec (Hunter 1973). Spawning hatchery kokanee in Lake Whatcom average 4 to 5 years of age and are typically no larger than 26 cm (Looff 1994). Most wild Lake Whatcom kokanee spawn in their third year, although some in the second and fourth years may spawn as well (WDNR 1998). Kokanee adults die after spawning. After emergence, kokanee fry generally migrate to Lake Whatcom within a few days (WDNR 1998). Kokanee typically move through the lake in schools. 3.3.2 Distribution The primary kokanee population in WRIA 1 occurs in Lake Whatcom and it s tributaries. Kokanee from the Lake Whatcom stock have also been introduced to Toad Lake in the Squalicum Creek system (Huddle 2001). 3.3.3 Periodicity After moving from the lake and into tributary streams, Lake Whatcom kokanee generally spawn from late August through January, although historically spawning continued through February (Looff 1994). The majority of spawning occurs from late October through early December. Alevins emerge between late January and March, then migrate downstream to the lake within a few days (WDNR 1998). 3.4 Rainbow Trout Rainbow trout (O. mykiss) are the non-anadromous form of steelhead trout. They are native to WRIA 1 although their distribution in the area has been broadened through hatchery plantings. Rainbow trout populations are also supplemented by the residual steelhead trout (i.e., offspring of anadromous steelhead trout that do not migrate to salt water). 3.4.1 Life History and Habitats Rainbow trout prefer well oxygenated and cool water, less than 21 C, although they tolerate a wide range of temperatures (Wydoski and Whitney 1979). They occur in rivers and lakes and may grow up to 71 cm (28 in). Juvenile rainbow trout occupy riffle areas during the summer and pool areas during the other seasons, typically remaining near the stream bottom. Most rainbow trout mature at three years of age, with a range of one and five years. Rainbow trout move into tributary streams to spawn. Redds are often built at the head of a riffle, just below a pool, in gravel Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 20

substrate (McPhail and Lindsey 1970). Rainbow spawning locations are typically 18 cm deep, with velocities between 48 and 91 cm/s and substrate between 0.6 and 5.2 cm (Smith 1973). 3.4.2 Distribution Rainbow trout distributions in WRIA 1 are limited. Resident populations occur in upper reaches of all three forks of the Nooksack River. Rainbow trout in tributaries generally occupy higher reaches of streams, above cutthroat trout distributions in the lower reaches (FERC 1994). Rainbow trout populations developing through the steelhead trout residualism may occur in all areas of the Nooksack River system accessible to steelhead trout. Rainbow trout occurrence is not documented in the independent drainages. Rainbow trout were planted into Mirror Lake, in the Lake Whatcom watershed, as recently as the 1980 s but a sustainable population did not result (Johnston 2001a). Mueller et al. (1999) found 2 rainbow trout in Lake Whatcom sampling conducted in 1998. Rainbow trout are also found in Lake Padden (Johnston 2001a). 3.4.3 Periodicity After moving into tributary streams, rainbow trout spawn between February and May (Wydoski and Whitney 1979; Johnston 2001a). Eggs develop in the gravel for about 2 months and the young emerge during the summer. Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 21

4 NON-NATIVE NON-ANADROMOUS SALMONIDS IN WRIA 1 4.1 Eastern Brook Trout Eastern brook trout (S. fontinalis) is a char species that has been introduced to the Nooksack River system. There are reports that brook trout have spawned with bull trout/dolly Varden to produce hybrids (Huddle 2001; Hendrick 2001; Johnston 2001a). Brook trout occupy cool, clear rivers and lakes. They thrive in water temperatures below 20 C with an optimum range of 13 to 19 C (Wydoski and Whitney 1979). They are the only char found in the North Fork above Nooksack Falls (RKm 105; Johnston 2001a). Brook trout typically spawn from late October to December in tributary streams (McPhail and Lindsey 1970). Fry emerge from the gravel in early spring and remain near the nest through their first summer. 4.2 Brown trout Brown trout (Salmo trutta) occurrence in WRIA 1 is limited to a population introduced to Squalicum Lake (Johnston 2001a). 5 NATIVE NON-SALMONIDS IN WRIA 1 5.1 Lamprey Three species of lamprey are known to occur in WRIA 1, Pacific lamprey (Lampetra tridentatus), river lamprey (L. ayresi), and western brook lamprey (L. richardsoni). Pacific lamprey are currently listed as a Species of Concern by the U.S Fish and Wildlife Service (USFWS). Little information is known about the abundance or biology of lamprey in the Nooksack River system, although research along the Pacific Coast of Canada and the Columbia River provides general information. It is not clear how river flows affect lamprey upstream movements, but they are considered weak swimmers compared to other fish (Close et al. 1995). 5.1.1 Life History and Habitats The generalized life history model for lamprey includes a larval stage in which the larvae (or ammocoetes) inhabit the fine sediments in shallow backwater areas and stream eddies for an extended period of time (approximately 5 years for Pacific lamprey; Russell 1986, Beamish and Northcote 1989) before metamorphosing into the adult form. As ammocoetes, lamprey do not have eyes or teeth and their mouth in enclosed by a hoodlike flap that is used for filter feeding (Wydoski and Whitney Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 22

1979). Pacific and river lamprey are anadromous species that are parasitic and feed on fish in the marine environment. Pacific lamprey size averages 5 inches when they enter saltwater (Beamish 1980). Pacific lamprey are known to remain in saltwater for up to 3.5 years (Beamish 1980) and reach lengths of 76 cm (30 in). River lamprey reach an average length of 30 cm (12 in). Western brook lamprey remain in freshwater throughout their lives and are much smaller at maturity than the other species (typically less than 18 cm [7 in]). After metamorphosis into the adult form, western brook lamprey do not feed; their only function is to reproduce. Pacific lamprey spawn in riffles, where they excavate a shallow depression in gravel (McPhail and Lindsey 1970). Less is known about river lamprey spawning, although they likely spawn in small nest dug in the sand and gravel of riffles. Western brook lamprey also spawn in riffles on rock, sand, or gravel substrate. Multiple lamprey pairs may spawn on a nest site. Pacific lamprey spawning locations can overlap those of salmonids and lamprey nests can appear similar to steelhead trout redds (Huddle 2001). Adults die soon after spawning. 5.1.2 Distribution Little information is known about the distribution of lamprey in the Nooksack River system. Pacific and river lamprey are likely to occur throughout the anadromous zone, and they may have the ability to pass barriers by slowly ascending the walls of dams (Wydoski and Whitney 1979). Western brook lamprey may be throughout the system, although no record of lamprey occurrence above anadromous barriers was found. Lamprey occurrence in the system can be characterized as not common, but scattered throughout the anadromous zone (Huddle 2001; Hendrick 2001). Specific documented occurrences include in the South Fork Nooksack River and Hovander Park on the mainstem near Ferndale (approximately RKm 7.6) screw traps operated by the Nooksack Tribe and Lummi Nation, respectively. Lamprey are caught in low numbers throughout the sampling period at these traps (MacKay 2001, Hovesak 2001), which has extended from as early as the start of January in the South Fork to the end of August at the lower mainstem. These traps sample the surface 120 cm (4 ft) of the channel thalweg, thus catching downstream moving individuals. Catches tended to be higher during night sets (MacKay 2001). Lamprey have been found in Whatcom Creek and Squalicum Creek which drain Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 23

directly into Bellingham Bay (Huddle 2001) and are assumed to occur in other independent drainages in the WRIA. 5.1.3 Periodicity Based on Pacific lamprey research, anadromous lamprey adults begin upstream migrations between April and June (Beamish 1980) and most spawning occurs during June and July (Wydoski and Whitney 1979). Upstream migrations and spawning is complete by September (Beamish 1980). Eggs hatch from the shallow nests in 2 to 3 weeks depending upon water temperature. Ammocoetes remain in the fine sediments for several years. Metamorphosis to adult form is believed to occur between July and October (Richards 1980; Beamish 1980). After completing metamorphosis, young adults migrate to saltwater between autumn and spring. In the Nicola River system in British Columbia, peak outmigration occurs in April and May (Beamish and Levings 1991). Outmigration of young adults and dispersal of ammocoetes is associated with increased flows (Beamish and Levings 1991). Western brook lamprey spawn from April to June, with a peak in May (Wydoski and Whitney 1979). Eggs hatch in about 10 days at water temperatures of 10 to 16 C. Ammocoetes remain in the fine sediments for several years. 5.2 Sturgeon Two species of sturgeon are known to occur in WRIA 1, white sturgeon (Acipenser transmontanus) and green sturgeon (A. medirostris). Little information is known about the abundance or biology of sturgeon in the Nooksack River system, including no documented occurrences of their spawning in the system. 5.2.1 Life History and Habitats Both species of sturgeon occurring in the Nooksack River are anadromous and long-lived. Green sturgeon spend more time in salt water than white sturgeon and are probably tidewater spawners (Fox 1994). Sturgeon are repeat spawners that first spawn in the spring of their third year, from mid-april to mid-june (Devore 1993). Their eggs are adhesive and they prefer to spawn on a cobble substrate in clean, silt-free moving water. Sturgeon are typically found in large river systems and tend to be found in the deeper holes of the river (Wydoski and Whitney 1979). Sturgeon undergo coastal Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 24

migrations along the western coast of the Pacific Northwest and Canada. They are believed to move between river systems as part of their normal feeding range, such that sturgeon from other large river systems (e.g., Fraser, Skagit, and Stilliguamish) may occur in the Nooksack River (Hendrick 2001). White sturgeon are the largest fish found in the freshwaters of North America, as specimens have been reported to reach a length of 609 cm (20 ft) and a weight of 816 kg (1,800 lbs; Wydoski and Whitney 1979). Average lengths of 20-yr old white sturgeon from the Columbia River are 178 cm (5.8 ft). Green sturgeon attain sizes as large as 210 cm (7 ft) and 158 kg (350 lbs), but most are less than 120 cm (4 ft) and 23 kg (50 lbs). 5.2.2 Distribution Sturgeon observations in the WRIA have been limited to the lower Nooksack River, below Ferndale (RKm 9.6). However, sturgeon movements into more upstream locations in the river and any spawning in the system have not been studied and cannot be ruled out. The observed movements of sturgeon are assumed to be individuals on feeding runs following longfin smelt into the river. 5.2.3 Periodicity Known sturgeon use in the Nooksack River is believed to be limited to between October and March (Devore 1993). Peak migrations of the longfin smelt they follow up the river occur in November. Spawning activities, which are not documented in the system, occur between mid-april and mid-june. 5.3 Mountain Whitefish Little information is available on mountain whitefish (Prosopium williamsoni) biology in WRIA 1. General information from other river systems is used to provide an overview of the species. 5.3.1 Life History and Habitats Mountain whitefish are a resident species in WRIA 1, typically not exceeding 30 cm (12 in) in length and 11 years of age in Washington State (Wydoski and Whitney 1979). They occur in both lakes and streams, including some with fast water (McPhail and Lindsey 1970). Generally, they inhabit large streams with temperatures between 9 and 11 C. Mountain whitefish tend to use riffles during the summer and large pools during the winter (Wydoski and Whitney 1979). They Final Draft: Fish Distribution and Periodicity in WRIA 1 Page 25