Deschutes River Instream Flow Study Hydraulic & Habitat Modeling Results. July 2, Prepared for: Squaxin Island Tribe Natural Resources Dept.

Transcription

1 Deschutes River Instream Flow Study Hydraulic & Habitat Modeling Results July 2, 2013 Prepared for: Squaxin Island Tribe Natural Resources Dept. Prepared by: Caldwell & Associates Olympia, WA Deschutes IFIM Study Hydraulic & Habitat Model Results July

2 TABLE OF CONTENTS Page Introduction... 3 Study Objectives... 3 IFIM Study Area... 3 Study Reaches... 3 Habitat Survey Information... 4 Study Sites & Transect Locations... 4 Hydrology Assessment... 6 Estimated Flows at Study Sites... 7 Target Flows... 7 Data Analysis - Hydraulic Model... 7 Vail Study Site (River Mile 35)... 8 Military Road Study Site (River Mile 18) Lakeside Study Site (River Mile 7) Results - Habitat Model Steelhead Spawning Steelhead Juvenile Summer Rearing Cutthroat Juvenile/Adult Summer Rearing References Appendix A Study Site Maps Appendix B Study Site Photos Appendix C Habitat Preference Criteria Deschutes IFIM Study Hydraulic & Habitat Model Results July

3 Introduction Study Objectives The objectives of this study are to investigate the potential habitat benefits of possible future instream flow augmentation efforts in the Deschutes River watershed. The study objectives are to investigate the quantity of summer (low-flow) habitat for resident salmonids (cutthroat trout) and rearing juvenile anadromous salmonids (coho and steelhead) in the Deschutes River. It is recognized that summer water temperatures and groundwater and spring inflow also strongly affect fish habitat quality (Roberts et al. 2008), although they are not directly addressed in this study. At the request of the agencies, spawning winter steelhead were included in the analysis, because the summer period contains a portion of the egg incubation period. The scoping report was reviewed by the State Depts. Of Fish & Wildlife and Ecology, and the Weyerhaeuser Co., in Fall Final site and transect selection took place during May 2012, as spring flows receded. Transect selection was discussed and approved with the state agencies during August Data collection took place between May and November, Data reduction, quality assurance and hydraulic model calibration was done during fall and early winter A draft of this report was provided for agency review and comment in March The study investigators thank the landowners who allowed us access to the Deschutes River. These include the Weyerhaeuser Co., Paul Sparks, Tom Goldsby, Deb Lowe, the Capitol Land Trust and Lakeside Industries. IFIM Study Area The study area is the Deschutes River between Tumwater Falls (approximately River Mile (RM) 0) and Deschutes Falls (approximately (RM) 42). This comprises the area of river accessible to anadromous salmonids since the construction of the Deschutes Hatchery fish ladder at Tumwater Falls in Instream flows have been set by the Dept. of Ecology between November 1 and April 15, at a control station located at River Mile (RM) 3.4 (WDOE 1980). Flows between April 15 and October 31 are not set, although the stream is closed to further water withdrawals. This study focused on the closed, primarily low-flow, time period. Study Reaches Raines (2007) defined three geomorphic reach types in the study area, and noted that previous investigators (Collins (1994), Sullivan et al. (1987)) also defined similar reach types. The uppermost reach, the Upland Transition between the forested headwaters and the glacial plain, lies between Deschutes Falls (RM 42) and RM 34. Land use is predominantly forestry. The middle reach, Glacial Drift Prairie, lies between RM 34 and RM 16. Land use in this reach is predominantly agriculture, with some forestry and rural housing. The lowest reach, Ice Recessional Sands and Kettles, lies between RM 16 and Tumwater Falls, with a lower slope and a wider floodplain than the middle reach. Land use in this reach becomes increasingly suburban in the downstream reaches. Deschutes IFIM Study Hydraulic & Habitat Model Results July

4 Upland Transition Ice Recessional Sands and Kettles Glacial Drift Prairie Figure 1. Longitudinal profile of the mainstem Deschutes River to Deschutes Falls at RM 42, showing three broad geomorphic areas (approximate vertical exaggeration of x50) (from Raines 2007). Habitat Survey Information ATEC (2001) summarized fish habitat and channel condition information from Cramer (1997), Taylor (1999) and unpublished data from the Squaxin Island Tribe. Reach-scale stream survey data were aggregated into 26 longer channel reaches based on valley slope, valley width and confinement, geomorphic channel characteristics and humanconstructed constraints (such as bridges and railroad grades). Fish use and habitat conditions were summarized, and restoration opportunities noted, for each reach. The original stream survey data (Cramer 1997) may not exactly reflect current habitat types located at the sub-reach level. However, we expect that the general proportion of habitat types surveyed, and the reach characteristics of the aggregated reaches, will be a reasonable description of stream channel geomorphology and current habitat characteristics. This information was used along with reconnaissance surveys to locate study sites and transect locations. Study Sites & Transect Locations Field reconnaissance took place during the summer of 2011 to identify potential study sites and transect (cross-section) locations. Because of the mostly private ownership in the watershed, study site locations were also located where access was available. Longitudinal water temperature information was consulted to attempt to place the study sites in areas where cool-water refugia may also be present (Watershed Sciences 2004). Three representative study sites were identified: the Vail site at RM 35, the Military Road site at RM 18, and the Lakeside site at RM 5 (Figure 2). Deschutes IFIM Study Hydraulic & Habitat Model Results July

5 Figure 2. Deschutes instream flow study sites and USGS gage locations. Deschutes IFIM Study Hydraulic & Habitat Model Results July

6 Hydrology Assessment Hydrologic information was be summarized from the two USGS stream gages in the watershed: Deschutes River at E Street Bridge (USGS ) (RM 0.5) and Deschutes River near Rainier (USGS ) (RM 28.6) (Greenberg 2011) (Figure 1). The summary focused on the months between April and October. Table 1. Available USGS streamflow records in the Deschutes River watershed. Station Number Station Name Deschutes River near Rainier, WA Deschutes River at E St Bridge at Tumwater, WA Drainage Area (miles 2 ) 89.8 Period of Record 6/1/ /20/1975; 6/1/1980-7/31/1982; 7/8/ /31/1986 (seasonal only); 6/1/1987-9/30/1998; 10/15/1988-4/15/1999; 10/1/1999-9/30/ (annual max); Table 2. Summary statistics for daily flow records for two USGS gages in the Deschutes River watershed. Deschutes River near Rainier Average Daily (cfs) Maximum Daily (cfs) Minimum Daily (cfs) Median Daily (cfs) April May June July August Sept Oct Deschutes River at E St. Bridge, Tumwater Average Daily (cfs) Maximum Daily (cfs) Minimum Daily (cfs) Median Daily (cfs) April May June July August Sept Oct Deschutes IFIM Study Hydraulic & Habitat Model Results July

7 Estimated Flows at Study Sites The translation between monthly flows at the Rainier and E Street USGS gages and the study sites was made using the unit-area method. The Vail study site has a watershed area of 56.6 square miles, compared to 89.8 square miles for the Rainier gage, thus flows were adjusted by a factor of In addition, measured flows at the Vail site were also estimated from staff gage readings taken at the Weyerhaeuser Co. gage, just upstream of the study site and that gage s rating curve (S. Beech, Weyerhaeuser Co., pers. comm., 2012). The Military Road study site has a watershed area of square miles, and is downstream of the Rainier gage. Thus estimated flows were adjusted by a factor of The Lakeside study site measured a watershed area of square miles, compared to 162 square miles for the E Street gage, thus estimated flows were adjusted by a factor of (Groundwater inflow between our study site and the gage was found to be a factor in flow estimates, and is discussed in the results section.) Target Flows Target flows for the three planned flow measurements were roughly estimated as follows: Low flow target: to allow modeling of the lowest monthly minimum flow. Medium flow target: to allow modeling of the average or median May October flow. High flow target: to allow modeling of the maximum of the July September flows. April flows tend to vary widely over the month, and the DOE IRPP flows distinguish between April 1 and 15 and April (DOE 1980). Because the hydrologic data are monthly summaries, we recognized that average and maximum flow estimates for April may be higher than desired for the high flow targets. The outcomes of the flows that were actually measured and the resulting range of flows possible for the hydraulic model, are discussed under the results section for each study site. In general, the long dry summer period of 2012 allowed data collection at typical baseflow conditions at all three study sites. Higher flows were gathered opportunistically, and the range of potentially modeled flows differs between the three sites. Data Analysis - Hydraulic Model A hydraulic model was constructed and calibrated for each transect or group of transects. The hydraulic models were built using software (TRPA 1995). Model calibration details presented here were reviewed by the Departments of Ecology and Fish & Wildlife per Washington Instream Flow Study Guidelines (WDFW & WDOE 2008), as well as by other interested parties. Deschutes IFIM Study Hydraulic & Habitat Model Results July

8 Vail Study Site (River Mile 35) This site is in the Upland Transition geomorphic reach, and lies on the Weyerhaeuser Vail Tree Farm, upstream of Falls Creek and downstream of the Deschutes River (1000 Road) bridge crossing. The original site was planned to be just downstream of the bridge. However, further reconnaissance in March 2012 found access to a more typical, lessconfined reach just downstream. The study site was moved to this reach. A total of six transects were set in a contiguous reach, just upstream of a series of deep pools created by the river impinging on the valley wall. In general, the stream is fairly unconfined in this reach (ATEC 2001). Transects are numbered from upstream to downstream. All transect elevations are with respect to a single benchmark. Transect photos are in Appendix B. Table 3. Vail study site transect characteristics. Transect Habitat Type ID 1 Riffle 2 Lateral Scour Pool, small side logjam 3 Pool tailout/glide 4 Run/glide 5 Deeper Run/glide 6 Head of Riffle w/ cobble bar *This transect was added after others, thus is out of alphabetic order. A very small tributary enters the stream on the left bank, just upstream of Transect 3. Streamflow was measured at either less than one cfs, or was too low to measure, during data collection. Flow Measurements Data from four different flow levels was measured. All flow measurements had a complete set of water surface elevation data, and a flow/velocity data set from Transect 4. Two measurements had flow/velocity data sets at all transects. Substrate and cover data were collected at the lowest flow measurement. Measured flows, and flows estimated from USGS and Weyerhaeuser Co. rating curves, are shown in Table 4. Data collection is summarized in Table 5. Table 4. Measured and estimated flows at the Vail study site. ` Measurement Date 5/10/2012 5/30/2012 7/10/2012 9/11/2012 Measured at: Flows (cfs) Vail study site USGS Rainier gage Estimated from: Weyerhaeuser gage rating curve USGS Rainier gage Deschutes IFIM Study Hydraulic & Habitat Model Results July

9 Table 5. Data collection summary for the Vail study site. Vail Study Site RM 35 Date Water Surface Elevation Velocity Measurement Measured Flow (cfs) 5/10/ All Transects Transect 4 5/30/ All Transects All Transects 7/10/ All Transects All Transects 9/11/ All Transects Transect 4 All water surface elevations relate to a single benchmark. Target flows set prior to data collection set the low flow targets at cfs, the mid-flow target at cfs, and the high flow target at 190 cfs. The high-flow target was not quite achieved, although the calibrated hydraulic model will allow modeling of an adequate flow range. Due to the dry summer period in 2012, it is likely that the lowest flow measurement captures baseflow conditions at this site. Using standard methods, the flows measured should allow modeling from 7 to 380 cfs, assuming the velocities at the higher flows are reasonable (Bovee et al. 1998). Scaling this flow range up to the Rainier gage, a range of 11 to 603 cfs is calculated. Summary statistics in Table 2 show that this range covers the lowest minimum flows, as well as the median/average flows observed from April through October. It also covers the maximum daily flows observed between July and September. Water Surface Elevation Model A four-flow regression using the measured flows was used to calibrate the water surface elevation model. Calibration details are in Table 6 and Figure 2. Deschutes IFIM Study Hydraulic & Habitat Model Results July

10 Table 6. Calibration details for the Vail study site. Discharge (cfs) Deschutes IFIM Vail Study Site Calibration Details Summary Transect Best Estimate from Measured Data Stage (given) Stage of Zero Flow (SZF) * 98.44* 98.37* 98.38* * 97.94* Ratio of Measured to Predicted Discharge Mean Error of Stage-Discharge Relationship B-Coefficient of Stage-Discharge Relationship * Water surface elevations at the 90 cfs measurement were estimated from waters edge and depth/velocity measurements, due to equipment malfunction. Deschutes IFIM Study Hydraulic & Habitat Model Results July

11 Water Surface Elevation (ft) Vail Study Site RM Transect 152 cfs 91 cfs 44 cfs 18 cfs Figure 3. Water surface elevations at the Vail study site. The smaller drop in stage between 44 and 18 cfs at Transect 1, a shallow riffle, is most likely due to a higher proportion of inter-gravel flow at 18 cfs than was found at the other transects. Velocity Predictions Velocity predictions were developed using a one-flow velocity model. Velocity predictions were considered good if they were within 15%, or within 0.2 fps, of the measured value. Pairs of measured/predicted values in italic did not meet these standards. Transect 4 has four measured velocity sets (18, 44, 90 and 152 cfs), while all other transects have two (44 and 90 cfs). Because velocity patterns varied between measured flows, measured and predicted velocities at the other measured flow (i.e. 44 cfs) are not compared here. The higher calibration flow was preferred, but the lower measured flow was used if velocity predictions were better. Table 7 summarizes predicted velocities for the calibration flow range, and compares measured and predicted velocities at the calibration flow. Deschutes IFIM Study Hydraulic & Habitat Model Results July

12 Table 7. Velocity prediction summary for the Vail study site. Vail Study Site Transect 1 Calibration flow (cfs) 90 Predicted Predicted Predicted Measured Predicted Predicted Predicted Flow (cfs) Maximum (fps) Mean (fps) Minimum (fps) Transect 2 Calibration flow (cfs) 90 Predicted Predicted Predicted Measured Predicted Predicted Predicted Flow (cfs) Maximum (fps) Mean (fps) Minimum (fps) Transect 3 Calibration flow (cfs) 90 Predicted Predicted Predicted Measured Predicted Predicted Predicted Flow (cfs) Maximum (fps) Mean (fps) Minimum (fps) Transect 4 Calibration flow (cfs) 90 ` Predicted Predicted Predicted Measured Predicted Predicted Predicted Flow (cfs) Maximum (fps) Mean (fps) Minimum (fps) Transect 5 Calibration flow (cfs) 90 Predicted Predicted Predicted Measured Predicted Predicted Predicted Flow (cfs) Maximum (fps) Mean (fps) Minimum (fps) Transect 6 Calibration flow (cfs) 44 Predicted Predicted Measured Predicted Predicted Predicted Predicted Flow (cfs) Maximum (fps) Mean (fps) Minimum (fps) Overall, most velocity predictions were in the good category. The fair velocity predictions at Transect 1 (a shallow riffle) are most likely due to the large substrates present on the transect (large and small cobble, and small cobble/large gravel combinations) which made some velocity measurements between rocks, with concentrated flow and higher measured velocities. Velocity Adjustment Factors (VAFs) are not presented here, since a one-velocity model was used to generate predicted velocities. Deschutes IFIM Study Hydraulic & Habitat Model Results July

13 Proposed Transect Weighting Table 8 shows the proposed transect weighting. The ATEC (2001)habitat survey summary for the two reaches near the site found % pool/glide habitat and % riffle habitat. The proposed transect weightings are based on that proportion. Table 8. Proposed transect weighting, Vail study site. Transect Habitat Type Weighting (%) 1 Riffle 15 2 Lateral scour pool 17 3 Pool tailout 18 4 Glide 17 5 Glide 18 6 Head of riffle 15 Deschutes IFIM Study Hydraulic & Habitat Model Results July

14 Military Road Study Site (River Mile 18) This site lies in the Glacial Drift Prairie geomorphic reach, and is just downstream of the Military Road bridge crossing. Land uses in the study reach include agriculture and rural residential. Land at the site includes pasture and rural residential. Riparian areas on both sides consisted of hardwoods and brush. Shading levels were fairly high over most of this reach. Channel substrates were large and small cobbles with some areas of small boulders or small bedrock outcrops. Streambanks were mostly vertical and 5 to 10 feet in height. No instream woody debris was present. Transect Selection A reconnaissance survey of approximately 920 linear feet of channel at the study site found 61% run/glide habitat, 22% pool and 17% riffle habitats. These results are similar to those presented by ATEC (2001) for the reach between RM 14.7 and 18.1, who found 37 percent pool/glide habitat, and 63% riffle habitat, which probably includes shallow glide habitat. A total of five transects were located in this reach. Numbering is from upstream to downstream. Table 9. Military Road study site transect characteristics. Transect Habitat Type ID 1 Riffle 2 Glide w/bedrock outcrop pool 3 Riffle 4 Glide 5 Glide All transect elevations are with respect to a single one benchmark. Flow Measurements Data from three different flow levels was measured (Table 10). All measurements had a complete set of water surface elevation data and flow/velocity data. Table 10. Measured and estimated flows at the Military Road study site. Military Road study site Measurement Date 7/2/2012 7/19/2012 8/27/2012 Measured at Flows (cfs) USGS Rainier gage Military Rd. study site Estimated at study site from USGS Rainier gage (cfs) Deschutes IFIM Study Hydraulic & Habitat Model Results July

15 Target flows set prior to data collection set the low flow targets at cfs, the mid-flow targets at cfs, and the high flow targets at cfs. As with the Vail site, it is likely that summer baseflow conditions were captured at the 41.5 cfs measurement. The highest flow measured, 98.5 cfs, is lower than preferable, but using standard methods the hydraulic model should be able to predict habitat conditions between 17 and 245 cfs. Scaling these measured flows down to the flows observed at the Rainier gage (Table 2) gives a range of flows at the gage of 14 to 206 cfs. This range covers minimum observed flows and median/average flows for all months but April. This range does not cover the maximum observed flows, although July through September maximum flows are not much higher than the upper range of the hydraulic model. Hydraulic Model Calibration Water Surface Elevation Model A three-flow regression using the measured flows was used to calibrate the water surface elevation model. Calibration details are in Table 11 and Figure 3. All water surface elevations relate to the same benchmark. Table 11. Calibration details for the Military Road study site. Deschutes IFIM Military Road Study Site Calibration Details Summary Transect Discharge Best Estimate from Measured Data Stage (given) Stage of Zero Flow (SZF) Ratio of Measured to Predicted Discharge Mean Error of Stage-Discharge Relationship B-Coefficient of Stage-Discharge Relationship Deschutes IFIM Study Hydraulic & Habitat Model Results July

16 Water Surface Elevation (ft) Military Road Study Site RM cfs 74 cfs 41.5 cfs Transect Figure 4. Water surface elevations at the Military Road study site. Velocity Predictions Velocity predictions were developed using a one-flow velocity model, and were evaluated as described for the Vail study site. Table 12 summarizes predicted velocities for the calibration flow ranges, and compares measured and predicted velocities at the calibration flow. In general, the hydraulic model performed well. At Transect1, which is a riffle with some amount of angled flow, the underprediction of the mean velocity falls just barely out of the 15%/0.2 fps criteria. Deschutes IFIM Study Hydraulic & Habitat Model Results July

17 Table 12. Velocity prediction summary for the Military Road study site. Military Road Study Site Transect 1 Calibration flow (cfs) 98 Predicted Predicted Predicted Measured Predicted Predicted Flow (cfs) Maximum (fps) Mean (fps) Minimum (fps) Transect 2 Calibration flow (cfs) 74 Predicted Predicted Measured Predicted Predicted Predicted Flow (cfs) Maximum (fps) Mean (fps) Minimum (fps) Transect 3 Calibration flow (cfs) 98 Predicted Predicted Predicted Measured Predicted Predicted Flow (cfs) Maximum (fps) Mean (fps) Minimum (fps) Transect 4 Calibration flow (cfs) 98 Predicted Predicted Predicted Measured Predicted Predicted Flow (cfs) Maximum (fps) Mean (fps) Minimum (fps) Transect 5 Calibration flow (cfs) 98 Predicted Predicted Predicted Measured Predicted Predicted Flow (cfs) Maximum (fps) Mean (fps) Minimum (fps) Deschutes IFIM Study Hydraulic & Habitat Model Results July

18 Proposed Transect Weighting Habitat types observed in the 2011 reconnaissance survey were very similar to those summarized by ATEC (2001), although the 2011 survey distinguished between run/glide, pool, and riffle habitats, and the ATEC survey only between riffle and pool habitats. Even weighting between transects seemed to reflect both sets of results. Table 13. Proposed transect weighting, Military Road study site. Transect Habitat Type Weighting (%) 1 Riffle 20 2 Glide 20 3 Riffle w/riprap and bedrock 20 outcrop 4 Glide 20 5 Glide 20 Deschutes IFIM Study Hydraulic & Habitat Model Results July

19 Lakeside Study Site (River Mile 7) This site lies in the Recessional Sands and Kettles geomorphic reach, and is just south and east of the Olympia Airport. Land uses in the study reach are mixed, and include industrial, suburban, agriculture and forestry. Land use at the study site is forestry and agriculture; and on the left bank pasture with some scattered trees. Instream habitat is mostly glide, with one area of split channel and one large eddy pool. This reach has 8 to 10 foot high vertical streambanks consisting of unconsolidated glacial sediments. Stream substrates were predominantly small and large cobble. Riparian conditions of the right bank were mature timber, mostly conifer with some hardwoods (forested land use). Riparian conditions on the left bank consisted of reed-canary grass with some willows (pasture land use). Due to the stream width and the lack of riparian trees on the left bank, shading levels were fairly low in this reach. No instream large woody debris was present. Access to the river channel at this site was limited, due to steep eroding vertical streambanks. A total of five transects were set, two in separate locations and three contiguous transects at a third location. Transects are numbered from upstream to downstream, Table 14. Lakeside study site transect characteristics. Transect Habitat Type Benchmark ID 1 Glide #1 2 Glide #2 3 Deeper glide w/lateral pool, streamside logs 4 Shallow glide #3 5 Riffle crest Flow Measurements Data from three different flow levels were measured (Table 15). All flow measurements had a complete set of water surface elevation data. The two lowest flow measurements had a complete set of velocity measurements, while the highest measurement (168 cfs) had a velocity measurement at Transect 4. Data collection is summarized in Table 16. Table 15. Measured and estimated flows at the Lakeside study site. Measurement Date 7/12/2012 7/17/2012 9/5/12 11/8/2012 Measured at: Flow (cfs) USGS E Street gage Lakeside study site Estimated from: USGS E St gage Difference (cfs) Deschutes IFIM Study Hydraulic & Habitat Model Results July

20 Table 16. Data collection summary for the Lakeside study site. Lakeside Study Site Measurement Date Flow (cfs) 7/12/ Water Surface Elevation Velocity Measurement Transect 1 Transect 1 Transects 2-5 Transect 2 5 7/17/ /5/ All All Transects 11/8/ All Transect 4 only Under summer baseflow conditions, we found a fairly consistent ~20 cfs difference between measured flows at this study site and flows estimated from the E Street gage records, using the unit-area method. This is consistent with data reported by Sinclair and Bilheimer (2007), who studied groundwater interactions in the Deschutes River. They found a losing reach from RM 9.2 (Spurgeon Creek confluence) to RM 6.8, and a gaining reach from RM 6.8 to the E Street bridge (0.5). In August 2003, they measured a net gain of 22.8 cfs between RM 6.8 and the E Street bridge. (The Lakeside study site is at approximately RM 7.) Target flows set prior to data collection necessarily relied on summary statistics from the E Street gage (Table 2), and are overestimates, given the amount of inflow noted between the study site at RM 7 and the E Street gage at RM 0.5. Low flow targets were set at cfs. Mid-flow targets were ~200 cfs, and high flow targets ~ cfs. The summer low flow measurements capture baseflow conditions at this site. Even adjusting the target flow estimates downward to account for inflow between our site and the E Street gage, our high flow measurement is probably somewhat lower than desired. This is a result of the decision to make all measurements in one water year, and the fact that transects were not able to be established until June, The 168 cfs flow measurement was made between fall precipitation events. Using standard methods, the hydraulic model should be able to predict a flow range between 28 and 420 cfs at this site. Scaling this range of flows up to the E Street gage is likely to be less accurate than estimates from the upstream study sites, due to the difficulty in estimating the inflow between the site and the gage for the non-summer months. However, using the unit-area method and adding 20 cfs summer inflow, a range of flows at the E Street gage was calculated at 51 to 506 cfs (Table 2). The covers observed minimum and average/median flows for April through October, and maximum daily flows during July through September. Water Surface Elevation Model A three-flow regression using the measured flows was used to calibrate the water surface elevation model. Calibration details are in Table 17 and Figure 3. Deschutes IFIM Study Hydraulic & Habitat Model Results July

21 Table 17. Calibration details for the Lakeside study site. Deschutes IFIM Lakeside Study Site Calibration Details Summary Transect Discharge Best Estimate from Measured Data * 120* Stage (given) Stage of Zero Flow (SZF) Ratio of Measured to Predicted Discharge Mean Error of Stage-Discharge Relationship B-Coefficient of Stage-Discharge Relationship *These measurements were taken on different days (Table 16). Deschutes IFIM Study Hydraulic & Habitat Model Results July

22 Water Surface Elevation (ft) Lakeside Study Site RM cfs 120/124 cfs 70 cfs Transect Figure 5. Water surface elevations at the Lakeside study site. Transect 1 elevations relate to Benchmark #1, Transect 2 elevations to Benchmark #2, and Transects 3 through 5 to Benchmark #3. Each benchmark is assigned an arbitrary elevation of feet, and has no relation to the actual elevation of any other benchmark. The purpose of this figure is to illustrate that changes in stage at different flows are similar at each transect, which would be expected in a low-gradient mainstem reach. Velocity Predictions Table 18 summarizes predicted velocities for the calibration flow range, and compared measured and predicted velocities at the calibration flow. The hydraulic model calibrated well over this range of flows. Deschutes IFIM Study Hydraulic & Habitat Model Results July

23 Table 18. Velocity prediction summary for the Lakeside study site. Lakeside Study Site Transect 1 Calibration flow (cfs) 124 Predicted Predicted Measured Predicted Predicted Predicted Flow (cfs) Maximum (fps) Mean (fps) Minimum (fps) Transect 2 Calibration flow (cfs) 120 Predicted Predicted Measured Predicted Predicted Predicted Flow (cfs) Maximum (fps) Mean (fps) Minimum (fps) Transect 3 Calibration flow (cfs) 120 Predicted Predicted Measured Predicted Predicted Predicted Flow (cfs) Maximum (fps) Mean (fps) Minimum (fps) Transect 4 Calibration flow (cfs) 120 Predicted Predicted Measured Predicted Predicted Predicted Flow (cfs) Maximum (fps) Mean (fps) Minimum (fps) Transect 5 Calibration flow (cfs) 120 Predicted Predicted Measured Predicted Predicted Predicted Flow (cfs) Maximum (fps) Mean (fps) Minimum (fps) Deschutes IFIM Study Hydraulic & Habitat Model Results July

24 Proposed Transect Weighting Summarizing survey data from two aggregated reaches in this section of river (RM 5.5 to 8.4) ATEC (2001) found approximately 65% pool/glide habitat and 35% riffle habitat. Since only one transect at our study site is a riffle, reflecting this weighting might allow too much weight on a single transect. Therefore, equal weighting of transects is proposed (Table 19). Table 19. Proposed transect weighting, Lakeside study site. Transect Habitat Type Weighting (%) 1 Glide at pipeline crossing, BM Deeper glide, BM # Glide w/lateral pool, BM # Shallow glide 20 5 Riffle crest 20 Deschutes IFIM Study Hydraulic & Habitat Model Results July

25 Results - Habitat Model Habitat preference criteria for adult and juvenile salmonids were chosen by the Squaxin Tribe in consultation with instream flow specialists from the departments of Ecology and Fish & Wildlife (WDFW & DOE 2008). Candidate species included coho, winter steelhead and cutthroat trout. Habitat criteria are used to predict the relationships between habitat and flow at each study site. This relationship is expressed as a habitat index: Weighted Usable Area (WUA) vs. flow. Because this study focuses on the summer and early fall low-flow conditions, rearing lifestage preference criteria were proposed for resident cutthroat and steelhead juveniles. Use of coho juvenile criteria was not proposed, since the Washington agencies do not recommend it, and coho spawning timing is outside the period of focus for this study (WDFW/DOE 2008). After discussion, DOE and WDFW recommended the addition of steelhead spawning criteria, in case a potential issue with egg incubation flows during the low-flow period was identified. A summary of habitat criteria used in this analysis is in Appendix C. The habitat-flow relationship for each species/lifestage is developed over the range of calibration flows that are possible to model at each study site. This relationship must be analyzed in the context of existing (or historic, or potential future) hydrologic conditions. This further analysis has not yet been done. As future management questions are articulated, information in the habitat-flow relationships can be used in context with estimates of hydrologic conditions, along with other information (for example, location of cold-water inputs and water temperature regimes), to provide insight with respect to instream habitat and how it changes as flows or flow regimes change. Steelhead Spawning Steelhead gained access to the Deschutes River watershed with the construction of the Tumwater Falls fish ladder in Distribution of winter steelhead spawning habitat in the Deschutes was listed in 1994 as including the mainstem river up to Deschutes Falls (RM 42) as well as the Offut Lake outlet, Silver Springs outlet, Reichel, Fall, Mitchell and Johnson Creeks. The last three streams are in the vicinity of the Vail study site. Spawning timing was listed as from early January through early April (WDFW & WWTIT 1994, in Haring and Konovsky 1999). Deschutes River steelhead population status were not rated in the 2002 Salmonid Stock Inventory (SaSI) (WDFW 2002). The co-managers did not rate the population because Steelhead historically did not have access to the Deschutes River basin until a fish ladder was installed at Tumwater Falls in Chambers Creek winter steelhead have regularly been released into the Deschutes River to support fishery opportunities. There has never been any intent to establish a wild, naturally spawning winter steelhead population through these releases. In fact, this hatchery stock has been selected for fishery enhancement because of its early return and spawning timing, which differentiate it from native winter steelhead stocks. These characteristics are not well suited to natural spawning conditions in the Deschutes, and these fish are not expected to exhibit significant natural production. Therefore, Deschutes winter steelhead are not rated in ((WDFW 2002; S. Steltzner, Squaxin Island Tribe, pers. comm. 2013). Deschutes IFIM Study Hydraulic & Habitat Model Results July

26 Weighted Usable Area vs. flow results for steelhead spawning are presented in Figures 6 through 8, to document that their inclusion at the agencies request. No further analysis is presented because no management question with regards to steelhead incubation flows has been articulated. The affects of changes in flows (and thus changes in stage) that could potentially affect egg incubation after spawning can be analyzed using an effective spawning analysis (Bovee et al. 1998). This analysis compares recorded flows during a given year s spawning period with later flows during the incubation period, and estimates the amount of spawnable area that retains a specified water level over spawning gravels for the entire incubation period. The estimate of the amount of spawning area where incubation was deemed successful (i.e., had sufficient water depth) is the amount of effective spawning. Steelhead Juvenile Summer Rearing Results of Weighted Usable Area vs. flow relationships for juvenile summer rearing are presented in Figures 6 through 8, and Tables 20 through 22. WUA was calculated as a multiplied function (velocity preference x depth preference x substrate/cover preference). Appendix C gives the sources of the habitat criteria that were used. Cutthroat Juvenile/Adult Summer Rearing The cutthroat summer rearing depth and velocity criteria in the state Instream Flow Study Guidelines were developed from field observations in the Ohanapechosh River and Early Winters Creek (5 studies, 251 fish), and contained observation of juvenile and adult fish (WDFW/DOW 2008, Figures 16a, b). The substrate and cover preference criteria used were from the same report (Table 3, Generic Juvenile Salmon and Trout Cover/Substrate Preference Table). There are no species-specific preferences for cutthroat trout for substrate and instream cover. Iteration I The first estimation of cutthroat summer rearing habitat used the state criteria, and Weighted Usable Area was calculated as a multiplied function (Velocity preference x depth preference x substrate/cover preference). Results from this first iteration are presented in Figures 6 through 8 with the legend title CTT J/A Vel/Depth/Cover. This calculation method did not result in a function that changed very much over the range of flows modeled. On examination, it appeared that the relatively narrow range of preferred depths (Table C-1, Appendix C) and the low preference values for the instream cover/substrates observed at our study sites contributed to the low, and relatively unvarying, WUA values. This may be because there were only a few places within our study sites where there was any instream cover (mostly overhanging reed-canary grass) within the cover types in Table 3 (WDFW/WDOE 2008). This left most available cover to be medium- and large-sized cobble substrates, which do not have very high preference values as instream cover. Because this calculation method does not result in a flow/habitat function that would be very useful for analysis, a second iteration was done to calculate habitat by a different function. Deschutes IFIM Study Hydraulic & Habitat Model Results July

27 Weighted Usable Area (sq. ft / 1,000 ft) Iteration II The second iteration to calculate WUA made two assumptions. Because there is no speciesspecific cover preference information, it is unknown whether the WDFW/DOE generic cover preference table represents preferences of cutthroat trout in the Deschutes, who presumably have either adapted to historic cover conditions, or are accommodating to current ones. This iteration did not use the instream cover/substrate preference in the multiplied calculation. The second assumption was that, above a certain minimum depth, any stream volume with preferred velocities would be preferred habitat. The depth criteria used modified the WDFW/DOE depth curve by allowing the depth preference to stay at 1 above 2.05 feet, in order to let the velocity preference have a stronger influence on the WUA calculations (Table C-2, Appendix C). This describes habitat as a condition where fish rearing in the mainstem Deschutes are assumed to key in on areas with appropriate velocities once a certain minimum depth is present, and to simply accommodate to what instream cover is, or is not, available. Rearing fish were observed during field measurements (species unknown) in areas without substantial instream cover, and a relatively low level of instream cover was typical of all three study sites. Results from the second iteration are presented in Figures 6 through 8 with the legend title CTT J/A Vel/Open Depth. These results give a habitat-flow relationship with a similar pattern to the first iteration, but one that differentiates more between habitat available at various flows. This may be more value to managers in answering resource questions. Figure 6. Weighted Usable Area vs. flow relationships for the Vail study site. Vail Study Site RM Flow (cfs) Steelhead Spawning Steelhead Juvenile CTT J/A Vel/Depth/Cover CTT J/A Vel/Open Depth Deschutes IFIM Study Hydraulic & Habitat Model Results July

28 Table 20. Weighted Usable Area (WUA) vs. flow results for the Vail study site. WUA is expressed in square feet of habitat per 1,000 feet of stream. Cutthroat Juvenile/Adult Cutthroat Juvenile/Adult Flow Steelhead Spawning Steelhead Juvenile WDFW/DOE Velocity/Depth/ Cover WDFW/DOE Velocity/Open Depth/No Cover (cfs) WUA WUA WUA WUA Iteration I Iteration II Deschutes IFIM Study Hydraulic & Habitat Model Results July

29 Deschutes IFIM Study Hydraulic & Habitat Model Results July

30 Weighted Usable Area (sq. ft / 1,000 ft) Figure 7. Weighted Usable Area vs. flow relationships for the Military Road study site. Military Road Study Site RM 18 18,000 16,000 14,000 12,000 10,000 8,000 6,000 4,000 2, Steelhead Spawning Steelhead Juvenile CTT J/A Vel/Depth/Cover CTT J/A Vel/Open Depth Flow (cfs) Deschutes IFIM Study Hydraulic & Habitat Model Results July

31 Table 21. Weighted Usable Area (WUA) vs. flow results for the Military Road study site. WUA is expressed in square feet of habitat per 1,000 feet of stream. Cutthroat Juvenile/Adult Cutthroat Juvenile/Adult Flow Steelhead Spawning Steelhead Juvenile WDFW/DOE Velocity/Depth/ Cover WDFW/DOE Velocity/Open Depth/No Cover (cfs) WUA WUA WUA WUA Iteration I Iteration II , , , , , , , ,073 4, ,133 4, ,279 5, ,511 5, ,754 6, ,002 6, ,247 7, ,684 8, ,733 8, ,558 9, ,001 9, ,112 10, ,360 11, ,286 12, ,784 12, ,031 13, ,007 13, ,730 13, Deschutes IFIM Study Hydraulic & Habitat Model Results July

32 Weighted Usable Area (sq. ft / 1,000 ft) Figure 8. Weighted Usable Area vs. flow relationships for the Lakeside study site. Lakeside Study Site RM Flow (cfs) Steelhead Spawning Steelhead Juvenile CTT J/A Vel/Depth/Cover CTT J/A Vel/Open Depth Deschutes IFIM Study Hydraulic & Habitat Model Results July

33 Table 22. Weighted Usable Area (WUA) vs. flow results for the Lakeside study site. WUA is expressed in square feet of habitat per 1,000 feet of stream. Cutthroat Juvenile/Adult Cutthroat Juvenile/Adult Flow Steelhead Spawning Steelhead Juvenile WDFW/DOE Velocity/Depth/ Cover WDFW/DOE Velocity/Open Depth/No Cover (cfs) WUA WUA WUA WUA Iteration I Iteration II Deschutes IFIM Study Hydraulic & Habitat Model Results July

34 References Agua Tierra Environmental Consulting (ATEC) Deschutes River reach scale analysis and habitat survey: final data report. Prepared for Thurston County Water & Waste Management, Olympia, WA. Bovee, K.D., B.L. Lamb, J.M. Bartholow, C,B, Stalnaker, J. Taylor and J. Henricksen Stream habitat analysis using the Instream Flow Incremental Methodology. USGS Report USGS/BRD Accessible via the internet at Collins, B A study of rates and factors influencing channel erosion along the Deschutes River, Washington with application of watershed management planning. Report prepared for Squaxin Island Tribe Natural Resources Dept., Shelton, WA. Cramer, D.D Deschutes River reach scale analysis and habitat survey. Report prepared for Thurston County, Olympia, WA. Greenberg, J Deschutes River hydrology analysis (Draft). Memorandum dated June 9, Hydrologic Services Co., Bellingham, WA. Haring, D. and J. Konovsky Habitat limiting factors final report Water Resource Inventory Area 13. Washington State Conservation Commission, Olympia, WA. Raines, M Deschutes River mainstem bank erosion Prepared for Squaxin Island Tribe and Washington Dept. of Ecology, Shelton/Olympia, WA. Roberts, M., A. Ahmed and G. Pelletier Deschutes River and Capitol Lake and Budd Inlet temperature, fecal coliform bacteria, dissolved oxygen, ph, and fine sediment Total Maximum Daily Load (TMDL) water quality study findings and appendices. Dept of Ecology, Olympia, WA. Sinclair, K. A. and B. Bilheimer Assessment of surface water/groundwater interactions and associated nutrient fluxes in the Deschutes River and Percival Creek watersheds, Thurston County. Dept. of Ecology publication Olympia, WA. Sullivan, K., S.H. Duncan, P.A. Bisson, J.T. Hefner, J.W. Ward, R.E. Bilby and J.L. Neilson A summary report of the Deschutes River basin: Sediment, flow, temperature and fish habitat. Weyerhaeuser Co., Federal Way, WA. Taylor, K Deschutes River off-channel habitat inventory. Squaxin Island Tribe, Shelton, WA & Thurston County, Olympia, WA. Thomas R. Payne & Associates (TRPA) RHABSIM User s Manual. Arcata, CA. U.S. Fish & Wildlife Service (USFWS). 2010a. Flow-habitat relationships for spring and fallrun chinook salmon and steelhead trout spawning in the Yuba River. Sacramento Fish & Wildlife Office, Sacramento, CA. August, Deschutes IFIM Study Hydraulic & Habitat Model Results July

35 Washington Dept. of Ecology. (DOE) Deschutes river basin Instream Resources Protection Program including proposed administrative rules (WRIA 13). Olympia, WA. Washington Dept. of Fish & Wildlife and Washington Dept. of Ecology (WDFW & DOE) Instream Flow Study Guidelines. Version 2004, Error Correction Update Olympia, WA. Washington Dept. of Fish & Wildlife, Salmon and steelhead stock inventory (SaSI). Accessed via the internet in 2013 at fisheries/sasi/search.php?searchby=wria & search=13&orderby=species. Watershed Sciences, Aerial survey of the Deschutes River, Washington. Thermal infrared and color videography. Report to the Washington Dept. of Ecology. Corvallis, OR. Deschutes IFIM Study Hydraulic & Habitat Model Results July

36 Appendix A Study Site Maps Map A-1. Geomorphic reach types, study sites, and USGS stream gage locations. Deschutes IFIM Study Hydraulic & Habitat Model Results July

37 Map A-2. Vail Study Site Location Deschutes IFIM Study Hydraulic & Habitat Model Results July

38 Map A-3. Military Road Study Site Location Deschutes IFIM Study Hydraulic & Habitat Model Results July

39 Map A-4. Lakeside Study Site Location Deschutes IFIM Study Hydraulic & Habitat Model Results July

40 Appendix B Study Site Photos Vail Study Site Transect Photos All photos taken on May 30, 2012 at approximately 90 cfs calibration flow. Transect 1, looking from the left bank to the right bank. Deschutes IFIM Study Hydraulic & Habitat Model Results July

41 Transect 2. Right bank is a wide gravel bar. Taken May 29, Transect 3. Looking downstream. The small left bank tributary can be seen on the left. Deschutes IFIM Study Hydraulic & Habitat Model Results July

42 Transect 4, looking from the left bank across to the right bank. Transect 5, looking from the left bank across to the right bank. Deschutes IFIM Study Hydraulic & Habitat Model Results July

43 Transect 4, with the tape up, looking downstream. The gravel bar on the left bank of Transect 6 is the bright area in the upper right of the photo, and the bedrock outcrop that creates the riffle is on the left of that. Transect 5 lies approximately halfway between the gravel bar and Transect 4. Deschutes IFIM Study Hydraulic & Habitat Model Results July

44 Military Road Study Site Transect Photos This is looking downstream. Transect 1 crosses the riffle in the foreground, and Transect 2 crosses the stream immediately in front of the tree on the left bank. The pool created by the bedrock outcrop at Transect 3 is roughly contiguous with the patch of shade on the left bank. This photo is of the same reach, looking upstream. Transect 1 is just above the riffle in the upper portion of the photo, and Transect 2 between the riffle and the photographer, who is standing near Transect 3. The bedrock outcrop on the left portion of Transect 3 can be seen. (Photo: E. O Connell, NWIFC) Deschutes IFIM Study Hydraulic & Habitat Model Results July

45 This photo shows the left bank of Transect 4, and most of the glide habitat. Photo: E. O Connell, NWIFC) This photo is taken upstream of Transect 1, looking downstream, and shows the glide habitat typical of Transects 4 and 5, which lie downstream. Deschutes IFIM Study Hydraulic & Habitat Model Results July

46 Lakeside Study Site Transect Photos Lakeside Transect 1, taken from the right bank looking at the left bank. This transect is a pipeline crossing, with a reed-canary grass riparian area. Lakeside Transect 2, looking from the right bank to the left bank. This brushy riparian area is more typical of the reach as a whole, excluding agricultural areas. Deschutes IFIM Study Hydraulic & Habitat Model Results July

47 Lakeside Transects 3 and 4, looking upstream from Transect 5. The tape is up across Transect 3. This mixed reed-canary grass and brush/trees riparian area is typical of the reach as a whole. Deschutes IFIM Study Hydraulic & Habitat Model Results July