Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Contract No. W912EF-08-D-0005, Task Order DT04

FINAL

Prepared For: U.S. Army Corps of Engineers Portland District PO Box 2946 Portland, OR 97208-2946

Submitted: November 2018 Prepared By: Normandeau Associates, Inc. 1921 River Rd. Drumore, PA 17518 www.normandeau.com

Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Executive Summary The U.S. Army Corps of Engineers (USACE), Portland District sponsored an investigation in November 2017 at Cougar Dam, Oregon as part of the Willamette Valley Project Biological Opinion (BiOp) research needs. This investigation was designed to obtain direct survival and injury estimates on juvenile Chinook Salmon (Oncorhynchus tshawytscha) passed through a Regulating Outlet (RO) at three different conditions at Cougar Dam (CGR) to be used to inform design considerations of volitional fish bypass systems at high intake head dams. There is one RO with two intakes at CGR; both intakes are located at elevation 1,485 fmsl. Intake No. 2 was tested in December 2009 and the present investigation tested intake No. 1 at two gate openings (originally it was proposed to test three gate openings). Cougar Dam is a 519 ft (158 m) tall rock fill hydroelectric dam. It has a gated concrete spillway and powerhouse with two turbines totaling 25 megawatts of electric power. The dam impounds the South Fork McKenzie River about 42 miles (68 km) east of Eugene, Oregon creating Cougar Reservoir which has storage capacity of 219,000 acre feet (270,000,000 m3). The purpose of CGR is to provide flood risk management, hydropower, water quality improvements, irrigation, fish and wildlife habitat, recreation, storage, and navigation. As in the previous (2009) study, Normandeau utilized its HI-Z Turb’N Tag (HI-Z) tag recapture methodology to complete the objectives identified in the Detailed Scope of Work (DSW). Test fish for this study were obtained by the USACE from the Oregon State University (OSU) Wild Fish Surrogate Lab. All fish were transported to CGR using Normandeau’s provided fish transport truck equipped with a compressed oxygen system to keep fish alive during transport. Normandeau’s HI-Z tag technique was utilized to recapture test fish after passing through the RO tunnel. Sensor Fish equipped with HI-Z tags were also released with HI-Z test fish by Pacific Northwest National Laboratory to ascertain hydraulic and physical conditions of the passage route. The study was designed to release sufficient numbers of juvenile Chinook Salmon through the RO at two flow conditions (treatment) 1.3 ft RO headgate openings and 2.0 ft RO headgate opening to obtain survival estimates with a precision (α) level of ≤ ±0.03, 90% of the time and detection of a difference (∆) of 0.05 at α=0.05 and β=0.20 between survival estimates. The initial plan was to release a sufficient number of fish for each test condition (gate opening) at CGR to meet these goals; however, due to unexpected delays and time constraints all three test conditions could not be performed and the sample size was reduced for the 2.0 ft gate opening treatment. Direct survival at 1 and 48 hours (h) post passage was determined. The post passage condition of recaptured fish was evaluated by a malady-free metric, which accounted for fish free of visible injuries, loss of equilibrium, and/or > 20% scale loss. An injury-free estimate was also calculated which disregarded loss of equilibrium (LOE). Juvenile fish were equipped with two HI-Z tags and a radio transmitter then released through four-inch diameter hoses and pipes that directed them into the RO outlet tunnel that discharges

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon into a chute with guide walls that plunges at a steep angle (~70° slope) into a widened concrete plunge pool channel downstream. Upon project passage, the test fish were recaptured from the tailrace by one of two boats after the HI-Z tags inflated and buoyed the fish to the surface. All recaptured test fish were examined for injuries, tags removed, and then the fish were held in on-shore pools for 48 h post passage evaluation. A total of 227 treatment fish (size range 160 - 283 mm, mean 235 mm, total length) were released through the RO at 1.3 ft gate opening from 15-17 November and 51 juvenile treatment fish were released through the RO at 2.0 ft gate opening on 18 November. A total of 122 combined control fish (size range 173 - 279 mm, mean 233 mm) were released downstream of the plunge pool channel. Physical recapture of treatment fish ranged from 91.9% for the 1.3 ft gate opening to 96.1% for the 2.0 ft gate opening. Control fish recapture rate was 100%. The estimated 1 h survival for treatment fish passed at 1.3 ft gate opening was 97.3% (SE = 1.1%) and 88.2% (SE = 4.5%) for the 2.0 ft gate opening. Due to high control mortality (> 25%) the 48 h survival estimates were deemed unreliable and are referenced briefly in this report. The dominant physical injury type was ruptured or hemorrhaged eyes; 13.2% for fish passing through the RO at 1.3 ft gate opening and 8.1% for fish at the 2.0 ft gate opening. Operculum damage accounted for the next highest injury type; 7.7% at the 1.3 ft opening and 8.1% at the 2.0 ft opening. Injuries were primarily contributed to shear forces; however, concurrent Sensor Fish releases indicated only one incidence of shear. Malady-free rates of the treatment fish ranged from 48.5% (SE = 7.8%) for the 2.0 ft gate opening to 57.4% (SE = 3.9%) for the 1.3 ft gate opening. The injury-free rates were 83.2% (SE = 3.1%) and 88.6% (SE = 5.4%) for the 1.3 ft and 2.0 ft openings, respectively. The present study along with a previous study at the Cougar RO indicate that structures similar to the Cougar RO can provide valuable information that can be used to design volitional high head fish passage systems. The results of the live fish study and the hydraulic information from concurrent releases of Sensor Fish indicate that the RO chute likely contributed most to the observed injuries and making concrete bypass chutes as smooth as possible or covering them with a slick smooth coating should be considered.

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Survival Study Summary Framework

Year: November 2017

Study site: Cougar Dam RO

Objectives of study:

 Determine direct survival and malady-free estimates of juvenile salmonids upon passage through a Regulating Outlet at two different gate openings 1.3 and 2.0 ft

Fish:

 Species: juvenile Chinook Salmon (Oncorhynchus tshawytscha)

 Life stage: juvenile, 2-year old

 Source: Oregon State University (OSU) Wild Fish Surrogate Lab

Size (range & mean)

 Length (total length): range - 160 - 283 mm, mean 235 mm

Tag

 Type/model: HI-Z Balloon Tags

 Weight (gm): 1.9 g

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Table of Contents Executive Summary ...... i Acronyms and Abbreviations ...... vii Acknowledgements ...... ix 1.0 Introduction and Background ...... 1 1.1 Study Site Description ...... 1 1.2 Study Goals and Objectives ...... 1 1.3 Sensor Fish ...... 2 2.0 Methods ...... 8 2.1 Sample Size Requirements ...... 8 2.2 Source and Maintenance of Test Specimens ...... 8 2.3 Fish Tagging, Release, and Recapture ...... 9 2.4 Classification of Recaptured Fish ...... 10 2.5 Data Analysis ...... 11 3.0 Results ...... 23 3.1 Physical and Hydraulic Parameters ...... 23 3.2 Recapture Rates ...... 24 3.3 Fish Size and Recapture Times ...... 24 3.4 Passage Survival ...... 24 3.5 Injury Rate, Type, Severity, and Probable Cause ...... 25 4.0 Discussion ...... 32 5.0 Conclusions and Recommendations ...... 33 Literature Cited ...... 35 Appendix A: Derivation of Precision, Sample Size, and Maximum Likelihood Parameters .... 37 Appendix B: Short-term passage data...... 43 Appendix C: Detailed Fish Injury and Survival Data ...... 52 Appendix D: Survival and Malady-free Outputs ...... 59 Appendix E: Response to Agency Comments ...... 64

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

List of Tables

Table 2-1 Required sample sizes if control survival (S) is 1.00, 0.99, or 0.98, recapture rate (PA) is 0.99, 0.98, or 0.95 and expected survival (τ̂) of treatment fish passed is 0.95, 0.97, and 0.99 to achieve a precision level (ε) of ± 3.0%, 90% of the time...... 13

Table 2-2 Required sample sizes for detecting a statistical difference (Δ=τ1̂ -τ2̂ ) of 0.05 between two survival rates (τ1̂ and τ2̂ ) at α = 5.0% and 1-ß = 0.80. Table values also applicable for detecting differences between malady-free and injury-free estimates...... 13 Table 2-3 Actual daily schedule of released juvenile Chinook Salmon passed through the RO at 1.3 and 2.0 ft gate opening at Cougar Dam, November 2017. Controls released at the end of the RO channel...... 14 Table 2-4 Condition codes assigned to fish during passage survival and injury evaluations...... 15 Table 2-5 Guidelines for major and minor injury classifications for fish passage survival/injury studies...... 16 Table 3-1 Tag-recapture data and estimated 1 and 48 h survival, malady-free, and injury-free estimates for juvenile Chinook Salmon passed through the RO tunnel at Cougar Dam, November 2017...... 27 Table 3-2 Summary of visible injury types and injury rates observed on recaptured juvenile Chinook Salmon passed through the RO tunnel at the 1.3 and 2.0 ft gate opening at Cougar Dam, November 2017. Controls released at the end of the RO channel. Proportions are given in parentheses...... 28 Table 3-3 Probable sources and severity of maladies observed on recaptured juvenile Chinook Salmon passed through the RO tunnel at 1.3 and 2.0 ft gate opening at Cougar Dam, November 2017. Controls released at the end of the RO channel. Proportions are given in parentheses...... 29

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

List of Figures Figure 1-1 Cougar Dam powerhouse with rockfill dam in the background...... 3 Figure 1-2 Map of the Willamette River basin with Cougar Dam circled in red...... 4 Figure 1-3 Cross-section of the regulating outlet at Cougar Dam, Oregon provided by the USACE Portland District...... 5 Figure 1-4 Cross-section of the temperature control tower at Cougar Dam with the RO channel shown at elevation 1485 fmsl. Provided by the USACE Portland District...... 6 Figure 1-5 RO tunnel exit and chute which terminates in a plunge pool below...... 7 Figure 2-1 The HI-Z tags were activated and treatment fish were released through a 4- inch induction apparatus...... 17 Figure 2-2 The flexible 4-inch hose was attached to the PVC pipe just below the access above...... 18 Figure 2-3 The 4-inch PVC pipe terminated at a flexible hose downstream of the convergence of the two RO tunnels...... 19 Figure 2-4 Cross section of the RO at CGR with the induction system and flexible release hose shown in red...... 20 Figure 2-5 Plan view of the RO tunnel with the flexible release hose shown in red and the PVC release pipe shown in green...... 21 Figure 2-6 Boat crews were positioned downstream of the RO chute to recapture fish when buoyed to the surface...... 22 Figure 2-7 Juvenile Chinook Salmon were retrieved after the HI-Z tags inflated and buoyed the fish to the surface downstream of the RO chute...... 23 Figure 3-1 Length frequency distributions for treatment fish released through the RO at the 1.3 ft gate opening (blue bars), treatment fish released through the RO at the 2.0 ft gate opening (gray bars), and controls (orange bars)...... 30 Figure 3-2 Recapture time distributions for treatment fish released through the RO at the 1.3 ft gate opening (blue bars), treatment fish released through the RO at the 2.0 ft gate opening (gray bars), and controls (orange bars)...... 30 Figure 3-3 Examples of fish injuries observed for Chinook Salmon after passage through the RO at the 1.3 and 2.0 ft gate openings...... 31

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Acronyms and Abbreviations ATS Advanced Telemetry Systems

BiOp Biological Opinion

°C degree(s) Celsius

CENWP US Army Corps of Engineers Portland District

CGR Cougar Dam cfs cubic feet per second

DSW Detailed Scope of Work

El. Elevation fmsl feet above mean sea level ft/s or fps feet per second ft foot (feet) gal gallon

HI-Z HI-Z Turb’N Tag h hour(s)

IF injury-free in inch

LOE loss of equilibrium m meter(s)

MF malady-free mm millimeter(s)

PDT High Head Bypass Product Delivery Team

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

PNNL Pacific Northwest National Laboratory

RO regulating outlet

SE standard error

USACE U.S. Army Corps of Engineers

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Acknowledgements We thank the following people for their vital aspects to this study:

 U.S. Army Corps of engineers, Portland District: Fenton Khan  U.S. Corps of Engineers, Willamette Valley Project Office:  Biologists  Operational Staff at the project including operators, electrical, structural and maintenance crews were of great assistance throughout the course of the evaluation.  Oregon Department of Fish and Wildlife employees  Advanced Mechanical support

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

1.0 Introduction and Background The US Army Corps of Engineers Portland District (USACE) High Head Bypass Product Delivery Team (PDT) conducted a direct fish injury and mortality evaluation on Juvenile Chinook Salmon at Cougar Dam (CGR) to aid in making informed considerations of fish bypass systems for high head dams. The testing at CGR involved the recapture of fish when buoyed to the surface by HI-Z Tags (Heisey et al. 1992) after passing through a Regulating Outlet (RO). Normandeau employed the same methods for examining fish injury and survival as was used for previous fish injury and survival evaluations conducted at more than 60 power stations. 1.1 Study Site Description Cougar Dam is a 519-foot (158 m) tall rockfill hydroelectric dam in Oregon. It has a gated Regulating Outlet (RO) concrete spillway and a powerhouse with two turbines totaling 25 megawatts of electric power (Figure 1-1). The dam impounds the South Fork McKenzie River about 42 miles (68 km) east of Eugene, Oregon (Figure 1-2), creating Cougar Reservoir which has a storage capacity of 219,000 acre feet (270,000,000 m3). The purpose of CGR is to provide flood risk management, hydropower, water quality improvement, irrigation, fish and wildlife habitat, recreation, storage, and navigation. The RO at CGR has two intakes both located at elevation 1,485 fmsl, and RO intake No. 2 was tested in December 2009 (Normandeau Associates, Inc. 2010). The RO intakes are located behind the temperature control tower and are gravity fed conduits controlled by a hydraulically-powered vertical in-line knife gates situated inside the old intake tower (Figure 1- 3). The intakes converge together into one RO a short distance downstream of the control gates that runs through the dam and adjacent rock formations (Figure 1-4). The single 13.5 ft diameter outlet tunnel passes flow traveling approximately 500 ft before it discharges on the downstream face of the dam south of the powerhouse. The RO discharge port transitions into a chute with guide walls that plunges 235 ft at a steep angle (~70 degree slope) into a widened concrete plunge pool channel that transitions into a rip-rap channel downstream (Figure 1-5).

1.2 Study Goals and Objectives This study was designed to estimate direct injury and survival of juvenile Chinook salmon passed through the RO at two varying flow conditions and identifying the impacts of exposure to high velocities under these conditions. This evaluation was to provide information for design considerations of a volitional fish bypass system for high head dams, with a focus at CGR. The specific objectives for the CGR RO evaluation were to estimate the direct effects of passage through the RO at various gate openings (1.3, 2.0 and 2.5 ft). However, due to operational and time constraints the 2.5 ft gate opening was not tested. A sufficient number of juvenile salmon were to be tested such that precision (ɛ) of survival and injury estimates were within ±0.03, 90% of the time; a statistical difference of ±0.05, at a 95% confidence interval was detectible between treatments; and injuries could be classified to type, cause, and severity.

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

1.3 Sensor Fish One-hundred and eighteen of Pacific Northwest National Laboratory’s (PNNL) Sensor Fish packages were equipped with HI-Z Tags and released under identical conditions and timing as live HI-Z tagged test fish. The concurrent release of the Sensor Fish provides hydraulic data that can indicate the timing and location that observed injuries to the live fish may occur.

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Figure 1-1 Cougar Dam powerhouse with rockfill dam in the background.

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Figure 1-2 Map of the Willamette River basin with Cougar Dam circled in red.

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Figure 1-3 Cross-section of the regulating outlet at Cougar Dam, Oregon provided by the USACE Portland District.

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Figure 1-4 Cross-section of the temperature control tower at Cougar Dam with the RO channel shown at elevation 1485 fmsl. Provided by the USACE Portland District.

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Figure 1-5 RO tunnel exit and chute which terminates in a plunge pool below.

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

2.0 Methods 2.1 Sample Size Requirements A primary consideration of these experiments was to release and recapture an adequate number of fish to obtain direct survival and injury estimates within a specified precision level and detect differences between treatment conditions. A precision level (ε) of ±0.03, 90% of the time was established for the survival, malady-free, and injury-free estimates to meet the objective of the RO evaluations. Statistical differences between treatments of ±0.05, 95% of the time were established at for the juvenile fish tests conducted at the RO. The sample size is a function of the recapture rate (PA), expected passage survival (휏̂) or mortality (1휏̂), survival of control fish (S), and the desired precision (ε) at a given probability of significance (α). In general, sample size requirements decrease with an increase in control survival and recapture rates (Tables 2-1 and 2- 2). Only the magnitude of specific difference () between treatments to be detected and α level can be controlled by an investigator. As in previous similar investigations, in performing the sample size calculations, we assumed that capture data from daily replicate releases for treatment and control groups could be pooled separately (i.e., natural variability ơτ²=0). We calculated that with the following assumptions: a recapture rate of 0.98, control survival or malady-free rate of 0.99, expected RO passage survival or malady-free rate of 0.97, approximately 250 treatment/juvenile salmon would be needed for each test condition (Table 2-1). These sample sizes would also satisfy the objectives of detecting a 0.05 difference between treatments if control survival and recapture rates would be near 100%. Because the data in these studies were to be analyzed on a daily basis to test the adequacy of the sample size in fulfilling the statistical objective of the study, the number of fish released could be adjusted accordingly. This strategy has been successfully employed in previous studies involving the HI-Z tag recapture method (Normandeau Associates, Inc. et al. 2014a, b, 2015, 2017). A previous direct survival evaluation where approximately 150 juvenile salmonids were passed through the CGR RO per treatment condition attained 48 h survival estimates with precisions within ±0.05, 95% of the time (Normandeau Associates Inc. 2010). The embedded flexibility in the experiment enables adjustments in sample sizes and can prove beneficial during an investigation; fish can be allocated to other treatments to gain insight into specific concerns that may arise during the course of an investigation. Table 2-3 shows the number of fish actually used in the experiments for each treatment and control group at CGR. Because of time and operational constraints due to turbine maintenance required at the Cougar Station, a reduced sample size of juvenile Chinook salmon was released for the 2.0 ft gate opening test, and the desired precision was not attained. 2.2 Source and Maintenance of Test Specimens All live juvenile Chinook salmon for the direct survival and injury evaluations at CGR were provided by USACE from The Oregon State University (OSU) Wild Fish Surrogate Lab. All fish were transported to CGR using a fish transport truck equipped with a compressed oxygen system to maintain adequate oxygen levels during transport. Prior to each evaluation all fish were held for 24 hours after transport to allow for recovery from stress associated with handling and transport. All fish holding tanks were continuously supplied with ambient river water and

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon covered to prevent fish from escaping. Ambient river temperatures ranged from 7.0 to 8.0 degrees Celsius (Table 2-3).The treatment and control fish for a given day were randomly drawn from the holding pools, thereby assuring that all treatment and control groups were of similar size and condition. 2.3 Fish Tagging, Release, and Recapture Handling, tagging, and recapture techniques for the juvenile Chinook salmon followed those previously used for HI-Z tag direct survival/injury studies at other hydroelectric projects on the Willamette, Columbia and Snake River Basins (Heisey et al. 1992, Mathur et al. 1996, 2000, Normandeau Associates Inc. 2010). Procedures for handling, tagging, release, and recapture of fish were identical for treatment and control groups. All fish releases were made during daylight hours (0700 to 1700 hours). Briefly, groups of 5 to 10 fish were removed with a water sanctuary equipped net from holding tanks to the adjacent tagging site using a small tub full of water. Fish displaying abnormal behavior, severe injury, fungal infection, or descaling (> 20% per side) were excluded from tagging. The same fish selection criterion was applied to all treatment and control groups. Fish were anesthetized (< 5 minutes) and equipped with two uninflated HI-Z tags (Heisey et al. 1992) and a miniature radio transmitter tag.

HI-Z tags were attached via a stainless steel pin inserted through the musculature beneath the dorsal and adipose fins. A radio tag was attached in combination with the dorsal HI-Z tag (Heisey et al. 1992). A uniquely numbered VI tag (Visual Implant, Northwest Marine Technology, Inc., Shaw Island, Washington) was also inserted in the post ocular tissue for use in tracking 48 h survival of individual recaptured fish. Fish also received a fin clip to designate release location (test or control) in the event the VI tag became dislodged. HI-Z tagged fish were placed in covered 20 gal containers continually supplied with ambient river water until fully recovered from anesthesia (generally 30 to 45 minutes, minimum 20 minutes). After full recovery from anesthesia, fish were then transported in groups of 5 to 8 in 20 gal tubs to the release location and individually placed into an induction system, tags were activated, and the fish was released. HI-Z tags commenced inflation approximately two to four minutes after the fish was released.

All treatment and control fish were released through an induction apparatus situated on a deck above the RO tunnel at 1505 fmsl that consisted of a small holding basin attached to a four-inch diameter flexible hose (Figure 2-1). This flexible hose was deployed through a hatch that opened into the RO tunnel downstream of the headgates which control the flow through the RO. The flexible hose was attached to a four-inch diameter PVC pipe that was attached to the side of the RO tunnel (Figure 2-2). This pipe terminated approximately 105 ft downstream of the RO headgates and approximately two feet below the center of the RO tunnel (Figure 2-3). Based on USACE calculations, the terminus of the fish release pipe was approximately 2.5 ft above the surface of the water flowing through the RO tunnel at the two gate openings of 1.3 and 2.0 ft. A cross section of the RO showing the location of the induction system and a plan view of the fish release pipe is shown in Figures 2-4 and 2-5, respectively. The release hose/pipe was filled and flushed with river water at approximately 4cfs to ensure fish were transported quickly to the

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon desired release point. Control fish were released via a similar induction system in an area downstream of the RO discharge and channel.

Upon passage through the RO tunnel and channel, juvenile fish were tracked and retrieved when buoyed to the surface by one of two recapture boat crews (Figure 2-6). Boat crews were notified of the radio tag frequency of each fish upon its release. Only crew members trained in fish handling were used to retrieve tagged fish. To minimize crew bias, no crew was specifically assigned to retrieve either control or treatment fish.

Radio signals were received on a loop antenna coupled to an Advanced Telemetry System (ATS) radio receiver. The radio signal transmission enabled the boat crew(s) to follow the movement of each fish after passage and position the boats downstream for retrieval when the HI-Z tag(s) buoyed the fish to the surface (Figure 2-7). 2.4 Classification of Recaptured Fish The immediate post-passage status of an individual fish was designated as alive, dead, recovery of detached tag and pin only, or unknown. The following criteria have been established to make these designations: (1) alive—recaptured alive and remaining so for 1 h; (2) alive—fish does not surface but radio signals indicate movement patterns; (3) dead—recaptured dead or dead within 1 h of release; (4) dead—only inflated dislodged tag(s) are recovered, and telemetric tracking or the manner in which inflated tags surfaced is not indicative of a live fish; and (5) unknown—no fish or dislodged tags are recaptured, or radio signals are received only briefly, and the subsequent status cannot be ascertained.

Mortalities of recaptured fish occurring after 1 h were assigned 48 h post-passage effects although fish were observed at approximately 12 h intervals. Specimens were examined for descaling and injury, and those that died were necropsied to determine the probable cause of death. Additionally, all specimens alive at 48 h were closely examined for injury and descaling. The initial examination allows detection of some injuries, such as bleeding and minor bruising that may not be evident after 48 h due to natural healing processes. Injury and descaling were categorized by type, extent, and area of body (Table 2-4). Photographs of injured fish were taken if the fish expired or after the 48 h holding period of live fish with visible passage-related injuries.

Fish without visible injuries that were not actively swimming or swimming erratically at recapture were classified as “loss of equilibrium” (LOE). This condition has been noted in most past studies and often disappears within 10 to 15 minutes after recapture if the fish is not injured. A malady category was established to include fish with visible passage related injuries, scale loss (> 20% on either side), or loss of equilibrium. Fish that died within 1 h that had no observable maladies were designated as having died from unknown malady. Fish that survived beyond one hour free that were free of visible injuries, with less than 20% scale loss per side, and without loss of equilibrium were designated “malady-free”(MF). Fish free of visible injuries and having less than 20% scale loss per side were designated “injury-free” (IF). Loss of equilibrium (LOE) was disregarded in this IF metric.

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Visible injuries, scale loss, and LOE were also categorized as minor or major based on laboratory studies by PNNL et al. (2001) and Normandeau field observations (Table 2-5). 2.5 Data Analysis Survival, IF, and MF estimates were calculated for each test condition and adjusted for controls. The MF metric provides a standardized way to depict a specific passage route’s effects on the physical condition of entrained fish and is based solely on fish physically recaptured and examined.

Passage survival, IF, and MF rates for the fish after passage through the RO were estimated relative to the respective control rates using the likelihood model given in Mathur et al. 1996. Appendix A describes the likelihood model and provides statistical derivation of precision, sample size calculations, and likelihood parameters.

The estimators associated with the likelihood model are:

For estimating survival (ˆ )

푎 푅 = 푇 푐 푅푇푎푐

Where,

RT = number of fish released for the treatment condition;

aT = number of fish alive for the treatment condition;

Rc = number of control fish released;

ac = number of control fish alive.

For malady-free (MF)

푚푇퐸푐 푀퐹 = 퐸푇푚푐

Where,

ET = number of treatment fish examined for maladies

mT = number of treatment fish without maladies

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Ec = number of control fish examined for maladies

mc = number of control fish without maladies

MF rates are based on the proportion of recaptured fish without passage-related visible injuries, LOE, and/or scale loss (>20%) or fish with injuries that were not attributable to passage. Differences in fish survival and MF estimates between passage routes were tested using a two- tailed z-test (P=0.05 level). The formula for IF rate is the same as that of MF rate, but disregards loss of equilibrium (LOE).

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Table 2-1 Required sample sizes if control survival (S) is 1.00, 0.99, or 0.98, recapture rate (PA) is 0.99, 0.98, or 0.95 and expected survival (τ̂) of treatment fish passed is 0.95, 0.97, and 0.99 to achieve a precision level (ε) of ± 3.0%, 90% of the time.

Expected treatment survival (τ ̂ ) Recapture Control 0.95 0.97 0.99 rate (PA) survival Required sample size 1.00 200 146 90 0.99 0.99 256 205 150 0.98 314 264 212 1.00 257 205 150 0.98 0.99 314 264 212 0.98 373 325 275 1.00 436 390 342 0.95 0.99 496 451 405 0.98 556 514 469

Table 2-2 Required sample sizes for detecting a statistical difference (Δ=τ1̂ -τ2̂ ) of 0.05 between two survival rates (τ1̂ and τ2̂ ) at α = 5.0% and 1-ß = 0.80. Table values also applicable for detecting differences between malady-free and injury-free estimates.

Recapture probability (PA)

Control Survival rates Difference 0.95 0.98 0.99 survival τ̂1 τ̂2 (Δ=τ̂1-τ̂2) Required sample size 0.95 0.90 0.05 680 529 481 0.98 0.97 0.92 0.05 601 447 398 0.99 0.94 0.05 519 361 311 0.95 0.90 0.05 630 481 434 0.99 0.97 0.92 0.05 550 398 350 0.99 0.94 0.05 467 311 261 0.95 0.90 0.05 582 434 387 1.00 0.97 0.92 0.05 501 350 302 0.99 0.94 0.05 416 262 213

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Table 2-3 Actual daily schedule of released juvenile Chinook Salmon passed through the RO at 1.3 and 2.0 ft gate opening at Cougar Dam, November 2017. Controls released at the end of the RO channel.

Water Lot Treatment Combined Date Temperature Number Controls (°C) 1.3 ft 2.0 ft 2 11/15 7.0 92 8 3 11/16 8.0 40 50 4 11/17 7.5 95 40 5 11/18 7.0 51 24 Total 227 51 122

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Table 2-4 Condition codes assigned to fish during passage survival and injury evaluations.

Status code description * Turbine/passage-related malady 4 Damaged gill(s): hemorrhaged, torn or inverted 5 Major scale loss, ≥50% de-scaled 6 Severed body or nearly severed 7 Decapitated or nearly decapitated 8 Damaged eye(s): hemorrhaged, bulged, ruptured, or missing 9 Damaged operculum: torn, bent A No visible marks on fish B Flesh tear at tag site(s) C Minor scale loss, <50% de-scaled E Laceration(s): tear(s) on body or head (not severed) F Torn isthmus G Hemorrhaged, bruised head or body H LOE K Failed to enter system L Fish likely preyed on (telemetry, circumstances relative to recapture) M Substantial bleeding at tag site P Predator marks Q Other information R Replaced due to unrecoverable conditions T Trapped inside tunnel/gate well V Fins displaced, or hemorrhaged (ripped, torn, or pulled) from origin W Abrasion / Scrape Dissection codes 1 Shear 2 Mechanical 3 Pressure 4 Undetermined 5 Mechanical/Shear 6 Mechanical/Pressure 7 Shear/Pressure B Swim bladder ruptured or expanded D Kidneys damaged (hemorrhaged) E Broken bones obvious F Hemorrhaged internally J Major L Organ displacement M Minor N Heart damage, rupture, hemorrhaged O Liver damage, rupture, hemorrhaged. R Necropsied, no obvious injuries S Necropsied, internal injuries observed W Head removed 15 Normandeau Associates, Inc.

Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Table 2-5 Guidelines for major and minor injury classifications for fish passage survival/injury studies.

Classification Injury/Condition Major Minor

LOE Only Fish dies within 1 hour Fish survives beyond 1 hour No visible external or internal injuries Fish dies within 1 hour Fish survives beyond 1 hour

Any minor injury Fish dies within 1 hour Fish survives beyond 1 hour Hemorrhaged eye(s) <50% hemorrhaged >50% hemorrhaged Deformed pupil(s) Always considered major N/A Bulged eyes 1 or both eyes entirely bulged Only 1 eye slightly bulged Bruises >10% of body per side <10% of body per side Operculum tear >5% of operculum <5% of operculum Operculum folded under or torn off Always considered major N/A Bleeding from gills Always considered major N/A > 20%Scale loss Always considered major N/A Scrape (damage to epidermis) >10% per side <10% per side Cut/laceration Generally any cut/laceration Small flap of skin cut/torn Internal hemorrhage or ruptured organ Fish dies within 48 hours Fish survives beyond 48 hours Broken backbone Always considered major N/A Multiple injuries Dependent upon worst injury

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Figure 2-1 The HI-Z tags were activated and treatment fish were released through a 4-inch induction apparatus.

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Figure 2-2 The flexible 4-inch hose was attached to the PVC pipe just below the access above.

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Figure 2-3 The 4-inch PVC pipe terminated at a flexible hose downstream of the convergence of the two RO tunnels.

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Figure 2-4 Cross section of the RO at CGR with the induction system and flexible release hose shown in red.

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Figure 2-5 Plan view of the RO tunnel with the flexible release hose shown in red and the PVC release pipe shown in green.

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Figure 2-6 Boat crews were positioned downstream of the RO chute to recapture fish when buoyed to the surface.

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Figure 2-7 Juvenile Chinook Salmon were retrieved after the HI-Z tags inflated and buoyed the fish to the surface downstream of the RO chute. 3.0 Results 3.1 Physical and Hydraulic Parameters The headgate that discharged water into the RO tunnel was either opened to 1.3 ft or 2.0 ft, resulting an approximate discharge of 480 and 730 cfs, respectively. The evaluation was conducted with the Cougar reservoir partially lowered at an elevation of 1574 fmsl. Full pool elevation is 1699 fsml. The elevation of the RO headgates was 1485 fmsl, which resulted in hydraulic a head of 89 ft.

The estimated velocity of the water passing through the RO tunnel where the test fish were discharged from the four-inch pipe was calculated using Sensor Fish data from PNNL et. al. 2018 (Draft) and was between 49.9 and 51.6 feet per second (fps) for the 1.3 and 2.0 ft gate openings, respectively. The velocity of the water exiting the four inch release pipe was measured with a water velocity meter and ranged from 11.9 to 12.7 fps. Thus, the fish exiting the four inch release pipe could have experienced a sudden velocity differential of 38 and 39.7 fps for the 1.3 and 2.0 ft gate openings, respectively. 23 Normandeau Associates, Inc.

Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Water temperature in the holding pools ranged from 7.0 to 8.0 °C (Table 2-3). This water was supplied to the holding pools via pumps in the tailrace of CGR, so these temperatures were similar in-river conditions.

3.2 Recapture Rates A total of 227 juvenile Chinook Salmon were released through the RO at the 1.3 ft gate opening and 51 were released at the 2.0 ft gate opening. Fewer fish were released at the 2.0 ft gate opening due to time constraints and project operations. A pooled group of 122 Chinook Salmon were released as controls for the treatment conditions. Two hundred and twenty (96.9%) of the treatment fish released at the 1.3 ft gate opening, 49 (96.1%) of the treatment fish released at the 2.0 ft gate opening, and all of the control fish released were recaptured by boat crews downstream of the facility. Of the seven fish that were not recaptured after passage through the RO at the 1.3 ft gate opening, five were assigned a dead status based on recovery of inflated HI- Z tags without fish or stationary radio signals, and two were assigned an unknown status. The two missing fish after passage through the RO at the 2.0 ft gate opening were assigned a dead status based on recovery of inflated HI-Z tags without fish (Table 3-1).

3.3 Fish Size and Recapture Times Fish size was similar between the treatment and control groups. The fish released through the RO at the 1.3 ft gate opening ranged from 160 to 283 mm in total length with a mean of 234 mm. Total length ranged from 203 to 265 mm with a mean of 237 mm for fish released through the RO at the 2.0 ft gate opening. Controls were similar with total lengths ranging from 173-279 mm with a mean of 233 (Figure 3-1).

The average times from release to recapture (recapture times) for fish released through the RO at the 1.3 and 2.0 ft gate openings were 6 minutes (range = 2 - 86 minutes) and 12 minutes (range = 1- 248 minutes), respectively. The recapture time for controls ranged from 1-126 minutes with a mean of 3 minutes. All but four of the fish released for both treatment conditions and one of the controls were recaptured within 15 minutes (Figure 3-2).

3.4 Passage Survival Only one of the 227 fish released through the RO at the 1.3 ft gate opening was dead upon recapture, and another five were assigned a dead status based on the recovery of inflated HI-Z tags without fish (3) or stationary radio signals (2). There were two fish of which no information could be ascertained and were assigned an unknown status. Four of the 51 fish released through the RO at the 2.0 ft gate opening were recaptured dead, and two others were assigned a dead status based on the recovery of inflated HI-Z tags without fish. None of the 122 control fish were recaptured dead or assigned a dead status. This resulted in 1 hour survival estimates of 97.3% (SE = 1.1%) for the 1.3 ft gate opening and 88.2% (SE = 4.5%) for the 2.0 ft gate opening. The desired precision of ±3%, 90% of the time was only met for the 1 hour survival estimate at

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon the 1.3 ft gate opening, and the 1 hour survival estimates were significantly different at the α = 0.05 level. The higher standard error for the 1 hour survival estimate at the 2.0 ft gate opening could have been reduced by increasing the sample size (which was restricted by time and operating conditions during the study (Table 3-1).

An additional 73 fish released through the RO at the 1.3 ft gate opening and 19 fish released at the 2.0 ft gate opening died during the 48 hour holding period. However, 31 (25.4%)of the control fish also died during this period, resulting in 48 hour survival estimates with relatively low precision that did not fall within the desired level of ±3%, 90% of the time. Although these estimates are presented in Table 3-1 they should be considered only as indicating a trend for lower survival at the higher discharge. For consistency this protocol has been implemented for all HI-Z tag studies; survival estimates are not considered reliable if more than 20% of the control fish die.

3.5 Injury Rate, Type, Severity, and Probable Cause A total of 220 fish were examined for injuries after passage through the RO at the 1.3 ft gate opening along with 49 fish at the 2.0 ft gate opening. The physical condition of the nine fish that were not recaptured could not be determined and are not included in this section. Of the 220 fish recaptured after passing the RO at 1.3 ft gate opening, 19.5% displayed passage-related visible injuries. 14.2% of the 49 fish displayed passage-related visible injuries after passing the RO at the 2.0 ft gate opening. Four (3.3%) of the 122 examined control fish displayed visible injuries. The percentage of fish displaying only loss of equilibrium (LOE) was 27.2% for the 1.3 ft gate opening, 36.7% for the 2.0 ft opening and 4.0% for the control fish. Many of the treatment fish displayed multiple injuries (Table 3-2 and Appendices B and C).

The dominant physical injury type for fish passed at the 1.3 ft gate opening was eye damage (ruptured/hemorrhaged) at 13.2%, followed by operculum damage (7.7%), bruising on the head/body (1.4%) and scrapes on the head/body (0.4%). The dominant injury types for fish passed at the 2.0 ft gate opening were eye damage (8.1%) and operculum damage (8.1%), and scale loss accounted for 2.0% of the injuries (Table 3-2 and Figure 3-3).

The probable causal mechanism for many of the maladies observed for fish released through the RO at both gate openings could not be determined and were classified as unknown (27.3 and 40.8% of the fish released at the 1.3 and 2.0 ft gate openings, respectively. The cause for six control fish (4.9%) that displayed maladies was also unknown. These fish (both treatment and control) displayed LOE without any obvious visible external or internal injuries. Additionally, many of these fish died during the delayed assessment period. For maladies with causal mechanisms that could be determined, shear was the dominant cause for maladies for both gate openings (18.2 and 10.2% of the fish examined at the 1.3 and 2.0 ft gate openings, respectively). Approximately twice as many fish with maladies were classified as having minor maladies compared to those with major maladies, however, a large proportion of fish released through the RO at both gate

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon openings (15.5 and 18.4% for the 1.3 and 2.0 ft gate openings, respectively) were classified as having a major malady (Table 3-3).

The estimated MF rates for fish after passage through the RO at the 1.3 and 2.0 ft gate openings were 57.4% (SE = 3.9%) and 48.5% (SE = 7.8%), respectively. These MF rates did not fall within the desired precision level of ±3%, 90% of the time due to the large number of fish classified as having a malady, the small sample size for the 2.0 ft gate opening, and a relatively high incidence (7.4%) of maladies among control fish (Table 3-1).

The IF rates, which disregarded LOE, were considerably higher with values of 83.2% (SE = 3.1%) and 88.6% (SE = 5.4%) at the 1.3 and 2.0 gate openings, respectively. Although the 1 h survival estimates were significantly different these IF estimates were not significantly different. Additionally the 1 h survival (88.2%) and IF (88.6%) estimates for the 2.0 gate opening were almost identical (Table 3-1). Survival, MF, and IF statistical outputs as described in section 2.5 are provided in Appendix D.

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Table 3-1 Tag-recapture data and estimated 1 and 48 h survival, malady-free, and injury-free estimates for juvenile Chinook Salmon passed through the RO tunnel at Cougar Dam, November 2017.

Gate Opening (ft)

1.3 2.0 Controls 15-Nov 16-Nov 17-Nov Combined 18-Nov 15-18 Nov No. Released 92 40 95 227 51 122 No. Recaptured 86 (93.5%) 40 (100%) 94 (98.9%) 220 (96.9%) 49 (96.1%) 122 (100%) No. Alive 85 40 94 219 45 122 No. Dead 1 0 0 1 4 0 No. Assigned dead 4 0 1 5 2 0 Tag & Pin 2 0 1 3 2 0 Radio Telemetry 2 0 0 2 0 0 Unknown 2 0 0 2 0 0 Survival 1 h (%) 97.3* 88.2* SE (%) 1.1 4.5 No. Held 85 40 94 219 45 122 Died in Holding 31 23 19 73 19 31 Alive 48 h 54 17 75 146 26 91 Survival at 48 h (%) 87.0** 68.4** SE (%) 6.2 10.1 No. Examined 86 40 94 220 49 122 No. with Injuries 15 (17.4%) 7 (17.5%) 21 (22.3%) 43 (19.5%) 7 (14.3%) 4 (3.3%) Injury-free Rate (%) 83.2 88.6 SE (%) 3.1 5.4 No. with only LOE 21 12 27 60 18 5 No. with Maladies 36 19 48 103 27 9 Malady-free Rate (%) 57.4 48.5 SE (%) 3.9 7.8 * Estimates significantly different at α= 0.10. **48 h survival estimates are typically not presented if more than 20% of the control fish die (25% died).

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Table 3-2 Summary of visible injury types and injury rates observed on recaptured juvenile Chinook Salmon passed through the RO tunnel at the 1.3 and 2.0 ft gate opening at Cougar Dam, November 2017. Controls released at the end of the RO channel. Proportions are given in parentheses. Injury Type*

Passage- related visibly- Ruptured/ No. No. injured Scraped Operculum hemorrhaged Bruised Scale loss Date Released Examined fish head/body damage eye(s) head/body (>20%) LOE Only 1.3 ft Gate opening 15-Nov 92 86 15 (0.174) 0 (0.000) 5 (0.058) 11 (0.127) 2 (0.023) 0 (0.000) 21 (0.244) 16-Nov 40 40 7 (0.175) 1 (0.025) 4 (1.00) 2 (0.050) 0 (0.000) 0 (0.000) 12 (0.300) 17-Nov 95 94 21 (0.223) 0 (0.000) 8 (0.085) 16 (0.170) 1 (0.011) 0 (0.000) 27 (0.287) Totals 227 220 43 (0.195) 1 (0.004) 17 (0.077) 29 (0.132) 3 (0.014) 0 (0.000) 60 (0.272) 2.0 ft Gate opening 18-Nov 51 49 7 (0.142) 0 (0.000) 4 (0.081) 4 (0.081) 0 (0.000) 1 (0.020) 18 (0.367) Combined Controls 15-18 Nov 122 122 4 (0.032) 0 (0.000) 0 (0.000) 4 (0.032) 0 (0.000) 0 (0.000) 5 (0.040) *Some fish had multiple injury types

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Table 3-3 Probable sources and severity of maladies observed on recaptured juvenile Chinook Salmon passed through the RO tunnel at 1.3 and 2.0 ft gate opening at Cougar Dam, November 2017. Controls released at the end of the RO channel. Proportions are given in parentheses.

No. of Probable cause Severity fish Total with Mechanical/ Unknown examined maladies* Mechanical Shear Shear (LOE only) Minor Major 1.3 ft treatment 220 103 (0.468) 1 (0.005) 2 (0.009) 40 (0.182) 60 (0.273) 69 (0.314) 34 (0.155) 2.0 ft treatment 49 27 (0.551) 2 (0.041) 0 (0.000) 5 (0.102) 20 (0.408) 18 (0.367) 9 (0.184) Controls 122 9 (0.074) 0 (0.000) 0 (0.000) 3 (0.025) 6 (0.049) 2 (0.016) 7 (0.057) *Maladies include both visible injuries and LOE attributed to passage.

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30

25 1.3 ft. Treatment 20 Range: 160-283 mm Mean: 234 mm 15

10 2.0 ft. Treatment Proportion(%) Range: 203-265 mm 5 Mean: 237 mm

0 Controls Range: 173-279 mm Mean: 233 mm Total length (mm)

Figure 3-1 Length frequency distributions for treatment fish released through the RO at the 1.3 ft gate opening (blue bars), treatment fish released through the RO at the 2.0 ft gate opening (gray bars), and controls (orange bars).

40

35

30 1.3 ft. Treatment Range: 2-86 minutes 25 Mean: 6 minutes

20 2.0 ft. Treatment 15

Proportion(%) Range: 1-248 minutes 10 Mean: 12 minutes

5 Controls 0 Range: 1-226 minutes <1 1 2 3 4 5 6 7 8 9 10 >10 Mean: 3 minutes Recapture time (min)

Figure 3-2 Recapture time distributions for treatment fish released through the RO at the 1.3 ft gate opening (blue bars), treatment fish released through the RO at the 2.0 ft gate opening (gray bars), and controls (orange bars).

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Figure 3-3 Examples of fish injuries observed for Chinook Salmon after passage through the RO at the 1.3 and 2.0 ft gate openings.

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4.0 Discussion The failure to obtain reliable 48 h survival estimates for this study was due to the higher than expected mortalities of both control and treatment fish which died with no apparent injuries. The cause(s) for these mortalities is still under investigation. Although there were a few control fish that had injuries (3.3%) the subsequent death of 25.4% of the control fish during the 48h delayed assessment period could not be linked to hydraulic conditions at the control release site or environmental conditions in the fish holding pools. During a previous HI-Z tag study at the Cougar RO in 2009 (Normandeau Associated Inc. 2010) control juvenile Chinook Salmon were released at the same location downstream of the discharge from the RO and only 1 of 79 fish died and 2.5% were visibly injured.

The previous HI-Z tag study at the Cougar RO with juvenile Chinook Salmon (127-209 mm, mean 172 mm) was conducted with the RO flow control headgate opened 1.5 and 3.7 ft (Normandeau associates Inc. 2010). The fish were released upstream of the control headgate. The 1h survival rates at the 1.5 and 3.7 ft openings were 91.7% (SE = 2.2%) and 92.6% (SE = 2.1%) which was lower than that for the current 1.3 ft gate setting (97.3%, SE =1.1%) and higher than that for the current 2.0 ft gate setting (88.2% (SE = 4.5%). The 48h survival estimates at the 1.5 and 3.7 ft openings were 84.6 (SE = 2.4%) and 88.3% (SE = 2.5%), respectively. Although the 48h survival estimates for the present study could be biased because of the high 48h control fish mortality, the 48h survival estimates at the lower gate settings were similar between the previous (84.6%) and present (87.0%) studies. However, the 48h survival estimate was considerably lower at the higher gate settings for the present study (68.4%) than the previous study (88.3%). The percentage of fish with visible injuries was similar between the previous 1.5 ft opening (18.8%) and the current 1.3 ft opening (19.5%). The percentage of fish with visible injuries at the previous higher gate opening of 3.7 ft (20.5%) was slightly higher than the current 2.0 ft setting (14.3%); however smaller sample size and higher SE for estimates from the current test condition could bias this estimate. The frequency of the primary injury types did vary between the past and the present study. The dominant injury in the past study was opercula damage (11.0%), while 12.3% of the 269 fish from the current study had hemorrhaged/damaged eye(s) and 7.8% had opercula damage. In both the past and present studies most of the injuries we attributed to shear (13.3 and 17.5%, respectively) and a combination of shear and mechanical forces. Larger fish (>170 mm) had higher injury rates than smaller fish in the 2009 evaluation. Injury rates for fish were not dependent upon fish size for the present study, however, the fish used were larger than those used in the previous evaluation.

Although the fish for the present study were not subjected to the hydraulic forces at the flow control gate as occurred in the previous study the survival and injury rates were not markedly different. The previous study indicated that the hydraulic condition at the flow control gate particularly at the lower gate opening (1.5 ft) contributed to some of the injuries especially for the larger fish. The Sensor Fish data also indicated turbulent hydraulic conditions occurred at

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon the control gate which may have contributed to some of observed injuries to the fish. Based on the Sensor Fish hydraulic information from the present study, the fish injuries could have occurred when the fish exit the release pipe and enter the RO flow (Dent et al. 2018). Exit velocity is approximately 12 fps and vertical velocity at the point of entry into the RO flow after an approximately 3 ft drop is approximately 14 fps. Release pipe flow intercepted the RO flow in the tunnel traveling at approximately 49.9 fps or 51.6 fps when the headgate was open 1.3 ft and 2.0 ft, respectively. Nearly all Sensor Fish acceleration events in this location were attributed to strike due to the impact to the water surface from the vertical drop, and only one event in this region was attributed to shear. There were no other locations within the RO tunnel or chute of which the Sensor fish data showed zones of shear, which is contradictory to the results of the present study which indicate some fish experienced shear trauma within either the release system or the RO. Potentially injurious hydraulic conditions were also observed on the concrete chute at the end of the RO tunnel and also where the RO jet entered the discharge channel. 5.0 Conclusions and Recommendations The unexplained higher than expected mortality of both control and treatment fish during the 48h delayed assessment period warrants further investigation. The fish appeared to be in good health prior to the tests, however, within 24 hours of being tagged, released, and recaptured some fish without any apparent injuries began dying. The tagging procedures employed did not differ from those used for numerous other HI-Z tag studies on juvenile salmonids. One procedure to consider if similar mortalities occur in future investigations would be secure test fish from two different hatcheries. Another procedure to consider would be to tag a second group of control fish that would not be released into the river and held for a 48h observation period.

The relatively high differences (38-40 ft/s) between the water velocities at the terminus of the fish release pipe and the flowing water in the RO channel may have contributed to some of the shear injuries. These velocity differences should be reduced in any future testing if feasible; however Johnson et al. 2003 did indicate that discharge jet entry velocities of up to 50 ft/s (15.2m/s) should safely pass juvenile salmon at high flow outfalls.

The Sensor Fish severe events data (Deng et al. 2018) indicated that the RO chute likely contributed most to the observed fish injuries. The RO chute region generally had at least two times as many severe events (4.08 - 5.90 per release) as the other passage regions (0.76 – 1.94 per release). Smoothing the concrete surface of this chute or covering it with fiberglass reinforced polyethylene material would likely decrease the incidences of fish injury. Only one (0.8%) of 126 juvenile salmon passed through a new fiberglass reinforced polyethylene bypass chute at Chittenden Locks Washington was injured; that fish displayed a minor hemorrhaged eye (West Fork Environmental and Normandeau Associates Inc. 2017). This bypass structure had an operating head near 20 ft and passed approximately 125 cfs.

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The results of this study may be used to inform design considerations for volitional downstream fish passage at high head dams. Although this study only tested direct fish injury and survival for fish released downstream of the head gate of the RO, the data along with other fish injury and survival studies indicate that it may be possible pass downstream migrating juvenile fish through a conduit similar to the RO at CGR, however, further research is needed to guide design development.

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Literature Cited Heisey, P. G., D. Mathur, and T. Rineer. 1992. A reliable tag-recapture technique for estimating turbine passage survival: application to young-of-the-year American shad (Alosa sapidissima). Canadian Journal of Fisheries and Aquatic Sciences. 49:1826-1834.

Mathur, D., P. G. Heisey, E. T. Euston, J. R. Skalski, and S. Hays. 1996. Turbine passage survival estimation for Chinook Salmon smolts (Oncorhynchus tshawytscha) at a large dam on the Columbia River. Can. Jour. Fish. Aquat. Sci. 53:542-549.

Mathur, D., P. G. Heisey, J. R. Skalski, and D. R. Kenney. 2000. Salmonid smolt survival relative to turbine efficiency and entrainment depth in hydroelectric power generation. Journal of the American Water Resources Association 36:737-747.

Normandeau Associates, Inc., and J. R. Skalski. 2000. Evaluation of prototype shallow-flat flow deflector at Wanapum Dam spillbay 5 relative to chinook salmon smolt passage survival, 1999. Report prepared for Grant County Public Utility District No. 2. Ephrata, WA.

Normandeau Associates, Inc. 2010. Estimates of direct survival and injury of juvenile Chinook salmon (Oncorhynchus tshawytscha) passing a regulating outlet and turbine at Cougar Dam, OR. Report prepared for U.S. Army Corps of Engineers Portland District – Willamette Valley Project, Portland, OR.

Normandeau Associates, Inc. 2014a. Direct injury and survival of adult Steelhead Trout passing a turbine and spillway weir at McNary Dam. Report prepared for U.S. Army Corps of Engineers Walla Walla District, Walla Walla, WA.

Normandeau Associates, Inc. 2014b. Direct survival/condition of subadult and adult Rainbow Trout passing through a spillway and turbine at Albeni Falls Dam, Pend Oreille River, Idaho. Report prepared for U.S. Army Corps of Engineers Seattle District, Seattle , WA.

Normandeau Associates, Inc. 2015. Direct injury and survival of yearling Chinook Salmon passing the removable spillway weir following Ogee and deflector modifications to Spillbay 2 at Ice Harbor Dam, Snake River, 2015. Report prepared for U.S. Army Corps of Engineers, Walla Walla District, Walla Walla, WA.

Normandeau Associates, Inc. 2017. Direct injury and survival of Coho Salmon Smolt Through New and Existing Fish Bypass Flumes, Hiram M. Chittenden Locks, WA. Report prepared for West Fork Environmental 2350 Mottman Rd SW, Tumwater, WA.

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Pacific Northwest National Laboratory, BioAnalysts, ENSR International, Inc., and Normandeau Associates, Inc., 2001. Design guidelines for high flow smolt bypass outfalls: field laboratory, and modeling studies. Report prepared for Department of the Army, Portland District, Corps of Engineers, Portland, OR.

Deng et al, 2018. Willamette Valley High Head Bypass Downstream Passage Prototype Evaluation: Sensor Fish Evaluation of the Regulating Outlet at Cougar Dam. Final Report PNNL 27713 prepared for the U.S. Army Corps of Engineers, Portland District, Portland, Oregon, by Pacific Northwest National Laboratory, Richland, Washington.

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Appendix A: Derivation of Precision, Sample Size, and Maximum Likelihood Parameters

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The statistical description below is excerpted from Normandeau Associates, Inc. and Skalski (2000). For the sake of brevity, references within the text have been removed. However, interested readers can look up these citations in the report prepared by Normandeau Associates, Inc. and Skalski (2000).

The estimation for the likelihood model parameters and sample size requirements discussed in the text are given herein. Additionally, the results of statistical analyses for evaluating homogeneity in recapture and survival probabilities, and in testing hypotheses of equality in parameter estimates under the simplified (HO:PA=PD) versus the most generalized model

(HA:PAPD) are given. The following terms are defined for the equations and likelihood functions which follow:

RC = Number of control fish released

RT = Number of treatment fish released

R = RC=RT

n = Number of replicate estimates ˆi (i=1,…,n)

aC = Number of control fish recaptured alive

dC = Number of control fish recaptured dead

aT = Number of treatment fish recaptured alive

dT = Number of treatment fish recaptured dead

S = Probability fish survive from the release point of the controls to recapture

PA = Probability an alive fish is recaptured

PD = Probability a dead fish is recaptured  = Probability a treatment fish survives to the point of the control releases (i.e., passage survival) 1- = Passage-related mortality.

The precision of the estimate was defined as:

P(  ˆ   ) 1 or equivalently

P( |ˆ  | ) 1

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon where the absolute errors in estimation, i.e., |ˆ -  |, is < (1-) 100% of the time, ˆ is the estimated passage survival, and  is the half-width of a (1-) 100% confidence interval for or 1- . A precision of ±5%, 90% of the time is expressed as P(|ˆ -  |<0.05)=0.90.

Using the above precision definition and assuming normality of ˆ  , the required total sample size (R) is as follows:

 PZ  1   Var()()ˆˆ Var

 PZ /2  Var()ˆ

  /2  Var()ˆ

  Z Var()ˆ  /2

 2 ˆ Var( )  2 Z  1 2

2  (1 SPA ) (1 SPA )       2 . SPA  RT RC  Z  1 2 where Z is a standard normal deviate satisfying the relationship P(Z>Z1-/2)=/2, and  is the cumulative distribution function for a standard normal deviate.

If data can be pooled across trials and letting RC=RT=R, the sample size for each release is

2  Z1 / 2 R  1  2SPA  2 . SPA 

By rearranging, this equation can be solved to predetermine the anticipated precision given the available number of fish for a study. In most previous investigations (Normandeau Associates, Inc. and Skalski 2000) this equation has been used to calculate sample sizes because of

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon homogeneity between trials; in the present investigation sample size was predetermined using this equation.

If data cannot be pooled across trials the precision is based on

n n ˆ ˆ ˆ (1 i ) / n  1  i / n  1 . i1 i1

Precision is defined as

P(|ˆ  | ) 1

P(  ˆ  | ) 1

 Pt  1  n1 Var()()ˆˆ Var

 Pt /2 n1 Var()ˆ

  /2 Var()ˆ

   t / 2,n1 Var(ˆ)

 2 ˆ Var( )  2 t1 / 2,n1

2  (1S PAA ) (1 SP )   SP R R  2 ATC  2 nt1 / 2,n 1 where 2=natural variation in passage-related mortality.

Now letting RT=RC  (1S P ) (1 SP )  2 AA  2 SPA  R R   2 nt1 / 2,n 1

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon which must be iteratively solved for n given R. Or R given n where  (1 SP )  (1 SP )  SP A A R  A 2  n 2   2    t1 / 2,n1 

 (1 ) SP R  A 2  n 2   2    t1 / 2,n1 

2 (1 )  t1 / 2,n1  R   2 2 2  . SPA n   t1 / 2,n1 

The joint likelihood for the passage-related mortality is:

L (S, , PA, PD | RC, RT, aC, aT, dC, dT)=

R a d R a d  C (SP ) C ((1 S)P ) C (1 SP  (1 S)P ) C C C acdC A D A D

( RT )(SP )aT ((1 S)P )dT (1 SP  (1 S)P ) RT aT dT aT dT A D A D .

The likelihood model is based on the following assumptions: (1) fate of each fish is independent, (2) the control and treatment fish come from the same population of inference and share that same survival probability, (3) all alive fish have the same probability, PA, of recapture, (4) all dead fish have the same probability, PD, of recapture, and (5) passage survival () and survival (S) to the recapture point are conditionally independent. The likelihood model has four parameters (PA, PD, S, ) and four minimum sufficient statistics (aC, dC, aT, dT). Because any two treatment releases were made concurrently with a single shared control group we used the likelihood model which took into account dependencies within the study design

(Normandeau Associates Inc. et al. 1995). For any two treatment groups (denoted T1 and T2), the likelihood model is as follows:

L(S, , , P , P | R , R , R ,a ,d ,a ,d ,a ,d )  1 2 A D C T1 T2 C c T1 T1 T2 T2

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R a d R a d T1 T1 T1 T1 T1 T1 (a d )(S1PA ) ((1 S1 )PD ) (1 S1PA  (1 S1 )PD ) T1 T1

R a d R a d T2 T2 T2 T2 T2 T2 (a d )(S 2 PA ) ((1 S 2 )PD ) (1 S 2 PA  (1 S 2 )PD ) . T2 T2 This likelihood model has the same assumptions as stated in Normandeau Associates, Inc. and Skalski (2000) but has five estimable parameters (S,  1 ,  2 , PA, and PD). The survival rate for treatment T1 is estimated by and for treatment T2, by  2 . A likelihood ratio test with 1 degree of freedom was used to test for equality in survival rates between treatments and based on the hypothesis HO: = versus Ha:  . Likelihood models are based on the following assumptions: (a) the fate of each fish is independent; (b) the control and treatment fish come from the same population of inference and share the same natural survival probability, S; (c) all alive fish have the same probability, PA, of recapture; (d) all dead fish have the same probability, PD, of recapture; and (e) passage survival () and natural survival (S) to the recapture point are conditionally independent. The estimators associated with the likelihood model are: a R ˆ  T C RT aC

R d a  R d a Sˆ  T C C C T C RC dC aT  RC dT aC

ˆ dC aT  dT aC PA  RT dC  RC dT

ˆ dC aT  dT aC PD  . RC aT  RT aC

The variance (Var) and standard error (SE) of the estimated passage mortality (1-ˆ ) or survival (ˆ ) are: (1  SP  A) (1 SPA ) Var(1ˆˆ )  Var ( )   SPATC R R

SE(1ˆ)  SE(ˆ)  Var(1ˆ)

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Appendix B: Short-term passage data

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Short term passage survival data for recaptured juvenile Chinook salmon passed through Cougar RO, at Cougar Dam, November 2017. Controls released at the end of the RO channel.

Total Time No. HI-Z Status Codes Length Minutes tags Survival Fish ID (mm) Released Recovery at large recovered Code 1 2 3 4 11/15/2017 Treatment 1.3 ft Water Temp = 7.0°C Z16 204 9:46 9:52 6 2 1 8 * Z17 267 9:51 9:57 6 2 1 A Q Z30 222 9:35 9:42 7 2 1 A Z19 241 9:48 9:53 5 2 1 A Z20 271 9:43 9:50 7 2 1 H * Z21 242 9:45 9:50 5 2 1 A Z22 234 9:30 9:39 9 2 1 A Z23 236 9:40 9:43 3 2 1 A Z24 254 9:37 9:44 7 2 1 A Z25 265 9:41 9:47 6 2 1 A Z26 232 10:20 10:24 4 2 1 H * Z27 238 10:26 10:31 5 2 1 A Z28 234 10:21 10:25 4 2 1 A Z29 255 10:27 10:29 2 2 1 H * B98 235 10:22 10:29 7 2 1 A Z31 229 10:15 10:20 5 2 1 A Z32 211 10:16 10:21 5 2 1 H * Z33 181 10:13 10:17 4 2 1 8 * Z34 230 10:19 10:23 4 2 1 A Z35 233 10:24 10:28 4 2 1 H * Z36 262 10:29 5 Z Z37 233 11:04 11:08 4 2 1 H * Z38 254 11:06 11:09 3 1 1 A Z39 256 10:59 11:04 5 2 1 8 * Z40 247 11:00 11:05 5 2 1 A Z41 217 12:00 12:03 3 2 1 A Z42 234 10:58 11:02 4 2 1 A Z43 209 11:05 11:12 7 2 1 A Z44 235 11:33 11:39 6 2 1 H * Z45 231 11:34 11:41 7 2 1 A Z46 235 11:29 11:34 5 2 1 A Z47 252 11:27 11:33 6 2 1 H 9 * Z48 242 11:28 11:32 4 2 1 H * Z49 228 11:36 11:40 4 2 1 A Z50 263 11:30 11:34 4 2 1 A Z51 241 12:01 12:06 5 2 1 H 8 * Z52 242 11:59 12:04 5 2 1 A Z53 217 12:03 12:12 9 1 1 H 8 G * Z54 262 11:58 12:04 6 2 1 H * Z55 259 12:02 12:07 5 2 1 A Z56 224 12:08 12:12 4 2 1 A Z57 220 12:05 12:10 5 2 1 H 8 9 * Z58 246 12:10 12:15 5 2 1 9 *

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Z59 240 12:04 12:09 5 2 1 A Z60 240 12:09 1 3 Z61 244 12:25 12:29 4 2 1 A Z62 227 12:07 12:16 9 2 1 H * Z63 250 12:26 12:30 4 2 1 H * Z64 252 12:24 13:49 85 2 1 A Z65 250 12:27 12:32 5 2 1 A Z66 241 12:28 12:34 6 2 1 A Z67 227 12:29 12:35 6 2 1 A Z68 223 12:23 12:27 4 2 1 A Z69 240 13:03 13:10 7 2 1 8 * Z70 222 13:04 13:15 11 1 1 A B99 239 12:58 13:05 7 2 1 H * Z72 242 12:57 13:06 9 2 1 A Z73 255 13:00 13:07 7 2 1 H * Z74 225 13:02 13:07 5 2 1 H * Z75 247 12:59 13:05 6 1 1 A Z76 221 13:01 13:08 7 2 1 A Z77 212 13:05 13:12 7 2 1 A Z78 266 13:05 5 Z Z79 246 13:37 13:47 10 1 2 H 9 * Z80 237 13:35 13:48 13 1 1 A Z81 206 13:28 4 X Z82 262 13:32 13:39 7 1 1 A Z83 247 13:30 13:35 5 2 1 H * Z84 226 13:27 3 Z85 232 13:26 13:31 5 2 1 A Z86 237 13:31 13:36 5 2 1 A Z87 240 13:38 13:45 7 2 1 A Z88 227 14:34 14:41 7 2 1 A Z89 223 14:37 14:42 5 2 1 A Z90 236 14:30 14:40 10 2 1 A Z91 211 14:32 14:45 13 2 1 A Z92 228 14:27 14:31 4 2 1 H * Z93 239 14:23 14:26 3 2 1 A Z94 272 14:54 14:58 4 2 1 A Z95 264 14:21 14:24 3 2 1 A Z96 246 14:22 4 X Z97 235 14:33 14:40 7 2 1 A Z98 253 14:28 14:33 5 2 1 A Z99 232 14:53 15:00 7 2 1 H * S00 249 14:56 15:03 7 2 1 A S01 256 14:49 14:52 3 2 1 H * S02 226 15:07 15:12 5 2 1 H * S04 221 14:49 14:54 5 2 1 A S05 203 15:01 16:27 86 2 1 A S06 222 14:06 15:09 63 2 1 H * S07 216 14:03 14:10 7 2 1 H * S08 236 15:00 15:04 4 2 1 A S09 273 15:03 15:06 3 2 1 A Controls S12 215 16:21 16:23 2 2 1 A S18 217 16:19 16:22 3 2 1 A

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S19 250 16:08 16:11 3 2 1 A S20 255 16:10 16:21 11 2 1 A S21 257 16:12 16:17 5 2 1 A S22 237 16:14 16:29 15 2 1 A S23 254 16:17 16:29 12 2 1 A S24 229 16:04 16:10 6 2 1 A

11/16/2017 Treatment 1.3 ft Water Temp = 8.0°C S82 225 14:27 14:31 4 2 1 A S83 236 14:22 14:24 2 2 1 A S84 195 16:08 16:13 5 2 1 H S85 213 14:26 14:32 6 2 1 A S86 250 14:23 14:27 4 2 1 A S87 221 14:18 14:21 3 2 1 A S88 209 14:25 14:30 5 2 1 A S89 228 14:19 14:23 4 2 1 H S90 252 14:19 14:25 6 2 1 H S91 226 14:16 14:20 4 2 1 9 S92 258 14:23 14:28 5 2 1 H S93 160 14:49 14:52 3 2 1 A S94 215 14:51 14:55 4 2 1 A S95 239 14:53 14:59 6 2 1 A S96 245 14:54 14:59 5 2 1 A S97 198 14:52 14:57 5 2 1 A S98 257 14:57 15:02 5 2 1 A S99 238 14:56 15:00 4 2 1 H P00 244 14:57 15:02 5 2 1 H P01 246 14:50 14:55 5 2 1 H P02 223 15:30 15:35 5 2 1 8 P03 236 15:32 15:36 4 2 1 A P04 248 15:37 15:40 3 2 1 A P05 235 15:24 15:30 6 2 1 H P06 171 15:28 15:30 2 2 1 9 P07 237 15:27 15:31 4 2 1 A P08 226 15:23 15:27 4 2 1 A P09 242 15:25 15:34 9 2 1 H P10 254 15:31 15:36 5 2 1 A P11 243 15:29 15:33 4 2 1 A P12 225 16:04 16:10 6 2 1 A P13 200 16:05 16:11 6 2 1 9 P14 219 15:59 16:05 6 2 1 H P15 223 16:01 16:04 3 2 1 A P16 223 16:02 16:06 4 2 1 A P17 235 16:03 16:09 6 2 1 H P18 258 16:08 16:13 5 2 1 H P19 256 15:58 16:00 2 2 1 H P20 231 16:06 16:11 5 2 1 A P21 252 15:59 16:03 4 2 1 A

Controls S44 211 10:05 10:06 1 2 1 A S45 225 9:51 9:52 1 2 1 A S46 251 9:55 9:57 2 2 1 A S47 230 9:44 9:50 6 2 1 A 46 Normandeau Associates, Inc.

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S48 253 9:53 9:57 4 2 1 A S37 223 10:45 10:46 1 2 1 A S38 227 10:18 10:20 2 2 1 A S39 229 10:42 10:44 2 2 1 A S42 240 10:20 10:22 2 2 1 A S43 211 10:47 10:51 4 2 1 A S32 221 9:48 9:51 3 2 1 A S33 243 10:02 10:04 2 2 1 A S34 228 10:01 12:07 126 2 1 A S35 237 9:58 10:00 2 2 1 A S36 240 10:42 10:44 2 2 1 A S50 236 9:42 9:43 1 2 1 A S51 228 9:47 9:48 1 2 1 A S52 234 12:26 12:27 1 2 1 A S53 272 12:28 12:28 0 2 1 A S54 240 12:32 12:33 1 2 1 A S60 226 12:12 12:13 1 2 1 A S61 220 12:08 12:10 2 2 1 A S62 222 12:21 12:22 1 2 1 A S63 207 12:05 12:08 3 2 1 A S64 224 12:02 12:03 1 2 1 A S65 224 12:07 12:08 1 2 1 H S66 222 12:33 12:33 0 2 1 A S67 243 12:16 12:19 3 2 1 A S68 231 12:11 12:11 0 2 1 A S69 240 12:13 12:15 2 2 1 A S26 235 10:40 10:41 1 2 1 A S27 209 12:37 12:38 1 2 1 A S76 220 13:15 13:16 1 2 1 A S29 247 10:14 10:16 2 2 1 A S30 252 10:15 10:24 9 2 1 A S55 193 13:12 13:14 2 2 1 A S56 225 12:38 12:39 1 2 1 A S57 226 12:35 12:36 1 2 1 A S58 216 12:30 12:31 1 2 1 H S59 259 13:19 13:20 1 2 1 H S70 209 12:00 12:01 1 2 1 A S71 227 12:20 12:20 0 2 1 A S72 234 12:03 12:04 1 2 1 A S73 251 13:05 13:06 1 2 1 A S74 233 13:09 13:11 2 2 1 A S75 233 13:17 13:18 1 2 1 A S77 250 13:03 13:04 1 2 1 A S78 254 13:12 13:15 3 2 1 A S79 235 13:11 13:12 1 2 1 A S80 226 13:07 13:10 3 2 1 A

11/17/2017 Treatment 1.3 ft Water Temp = 7.5°C P24 241 9:17 9:21 4 2 1 H P25 226 9:28 9:32 4 2 1 A P26 261 9:24 9:27 3 2 1 A P27 212 9:22 9:26 4 2 1 A P28 240 9:20 9:25 5 2 1 H

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P29 255 9:13 9:17 4 2 1 A P30 218 9:14 9:18 4 2 1 A P32 240 9:15 9:20 5 2 1 H P33 220 9:18 9:24 6 2 1 A P35 224 9:26 9:28 2 2 1 A P36 229 9:24 9:29 5 2 1 A P37 196 9:27 9:34 7 2 1 H P38 239 9:18 9:23 5 2 1 H P39 223 9:50 9:59 9 2 1 H P40 232 9:22 9:25 3 2 1 H P41 283 9:46 9:58 12 2 1 A P42 212 9:48 9:52 4 2 1 A P43 222 9:53 9:59 6 2 1 A P44 186 9:51 9:59 8 2 1 8 P97 240 11:51 11:54 3 2 1 A P45 213 9:47 9:50 3 2 1 A P46 236 9:55 9:58 3 2 1 A P47 215 9:56 10:01 5 2 1 H P48 250 9:54 10:01 7 2 1 A P49 242 9:57 10:02 5 2 1 H P51 229 9:49 9:54 5 2 1 A P52 249 10:21 10:25 4 2 1 H P53 243 10:16 10:27 11 2 1 A P54 247 10:17 10:23 6 2 1 A P55 223 10:20 10:27 7 2 1 A P56 280 10:16 10:19 3 2 1 H P57 240 10:17 10:23 6 2 1 H P58 245 10:24 10:27 3 2 1 A P59 249 10:27 10:30 3 2 1 A P60 236 10:28 10:35 7 2 1 H P61 235 10:24 10:29 5 2 1 A P62 236 10:25 10:33 8 2 1 H 8 P63 208 10:29 10:33 4 2 1 H P64 239 10:51 10:54 3 2 1 A P65 246 10:50 10:53 3 2 1 H P66 258 10:58 11:05 7 2 1 H P67 233 10:54 10:58 4 2 1 A P68 228 11:00 11:05 5 2 1 A P69 195 10:57 11:00 3 2 1 A P70 227 10:52 10:56 4 1 1 H P71 193 10:55 11:09 14 2 1 H 9 P72 225 10:53 10:58 5 2 1 A P73 238 10:58 11:01 3 2 1 A P74 236 11:27 11:35 8 2 1 H P75 256 11:27 11:34 7 2 1 A P76 247 11:20 11:24 4 2 1 A P77 190 11:20 11:25 5 2 1 A P78 226 11:23 11:30 7 2 1 A P79 229 11:24 11:30 6 2 1 A P80 228 11:31 11:45 14 2 1 H P81 230 11:25 11:32 7 2 1 H P82 228 11:28 11:37 9 2 1 H P83 261 11:21 11:26 5 2 1 H P84 258 11:58 12:03 5 2 1 H 48 Normandeau Associates, Inc.

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P85 241 11:54 12:00 6 2 1 H P86 235 11:52 11:56 4 2 1 A P88 247 11:56 12:00 4 2 1 H P89 219 11:57 12:14 17 2 1 H P90 220 12:00 12:05 5 2 1 A P91 249 11:53 12:00 7 2 1 A P92 227 11:59 12:04 5 2 1 H P93 236 11:55 12:01 6 2 1 A P94 235 12:03 3 P95 212 12:01 12:05 4 2 1 H P96 215 11:51 11:57 6 2 1 A P98 222 12:41 12:45 4 2 1 9 P99 237 12:43 12:48 5 2 1 A R00 246 12:39 12:44 5 2 1 H R01 237 12:47 12:52 5 2 1 A R02 237 12:48 12:53 5 2 1 8 R03 247 12:47 12:51 4 2 1 A R04 212 12:43 12:48 5 2 1 H R05 220 12:45 12:51 6 2 1 A R06 195 12:40 12:44 4 2 1 8 R07 243 12:51 12:56 5 2 1 A R08 236 12:44 12:49 5 2 1 H R09 226 12:49 12:54 5 2 1 H R10 240 13:11 13:16 5 2 1 9 8 H R11 225 12:40 12:43 3 2 1 A R12 242 13:14 13:19 5 2 1 H 9 R13 236 13:16 13:22 6 2 1 9 8 R14 231 13:21 13:24 3 2 1 H R15 237 13:22 13:26 4 2 1 H R16 215 13:15 13:20 5 2 1 A R17 251 13:15 13:19 4 2 1 H R18 243 13:10 13:14 4 2 1 A R19 242 13:20 13:24 4 2 1 A R20 242 13:20 13:24 4 2 1 A R21 203 13:19 13:23 4 2 1 H R22 236 13:10 13:13 3 2 1 A Controls R23 211 14:37 14:38 1 2 1 A R24 245 14:33 14:34 1 2 1 A R25 223 14:20 14:21 1 2 1 A R26 208 14:35 14:36 1 2 1 A R27 241 14:25 14:27 2 2 1 A R28 258 14:31 14:33 2 2 1 A R29 223 14:15 14:17 2 2 1 A R30 237 14:28 14:30 2 2 1 A R31 217 14:27 14:29 2 2 1 A R32 235 14:29 14:34 5 2 1 A R33 245 14:13 14:14 1 2 1 A R34 243 14:10 14:12 2 2 1 A R35 214 14:22 14:25 3 2 1 A R36 211 14:17 14:18 1 2 1 A R37 243 14:18 14:20 2 2 1 A R38 237 14:12 14:15 3 2 1 A R39 254 15:01 15:05 4 2 1 A 49 Normandeau Associates, Inc.

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R40 235 15:00 15:01 1 2 1 A R41 215 15:04 15:07 3 2 1 A R43 243 14:48 14:51 3 2 1 A R44 220 14:49 14:51 2 2 1 A R45 227 14:52 14:54 2 2 1 A R46 239 14:46 14:48 2 2 1 A R47 223 14:57 14:59 2 2 1 A R48 236 15:03 15:04 1 2 1 A R49 230 14:54 14:55 1 2 1 A R50 232 15:23 15:33 10 2 1 A R51 173 15:29 15:31 2 2 1 A R52 223 14:55 14:57 2 2 1 A R53 256 15:36 15:39 3 2 1 A R54 206 15:28 15:29 1 2 1 A R55 268 15:25 15:27 2 2 1 A R56 221 15:43 15:46 3 2 1 A R57 279 15:26 15:27 1 2 1 A R58 241 15:31 15:33 2 2 1 A R59 245 15:41 15:42 1 2 1 A R60 243 15:39 15:41 2 2 1 A R62 250 15:22 15:25 3 2 1 A R63 246 15:33 15:37 4 2 1 A R42 232 14:51 14:52 1 2 1 A 11/18/2017 Treatment 2.0 ft Water Temp = 7.5°C R64 237 16:31 16:37 6 2 1 A R66 245 16:39 16:44 5 2 1 A R67 231 16:38 16:44 6 2 1 A R70 203 10:32 10:35 3 2 1 H R71 233 11:16 11:21 5 2 2 H R72 216 10:43 10:58 15 2 1 A R73 247 10:48 14:56 248 2 2 R74 226 10:54 11:01 7 2 2 8 R75 214 11:28 11:36 8 2 1 A R76 255 10:52 10:55 3 2 1 H R77 244 11:38 11:39 1 2 1 H R78 205 12:22 12:27 5 2 1 A R79 232 12:14 12:25 11 2 1 A R85 265 13:12 13:14 2 2 1 A R86 244 10:48 10:57 9 2 1 H R87 219 10:38 10:44 6 2 1 A R88 254 10:31 10:35 4 2 1 H R89 227 10:42 10:45 3 2 1 A R90 263 10:37 10:41 4 2 1 A R92 237 12:13 12:17 4 2 1 H R93 225 11:45 11:49 4 2 1 H R94 234 11:50 11:53 3 2 1 H R95 225 12:28 12:31 3 2 1 A R96 258 11:29 11:34 5 2 2 R97 257 11:44 11:47 3 2 1 A R98 225 12:52 12:56 4 2 1 H 9 R99 225 12:51 12:56 5 2 1 H 8 W00 252 12:21 12:25 4 2 1 A W01 248 12:43 12:47 4 2 1 H

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W02 241 12:43 12:46 3 2 1 H 9 8 W03 246 11:57 12:02 5 2 1 A W04 231 13:27 13:31 4 2 1 H W05 218 13:06 13:09 3 2 1 H W06 241 13:31 13:37 6 2 1 A W07 242 13:26 13:29 3 2 1 H W08 265 13:18 13:22 4 2 1 A W09 246 13:17 13:20 3 2 1 H W10 242 13:32 13:37 5 2 1 A R80 258 11:51 11:56 5 2 1 H R81 240 12:29 3 R82 233 11:56 12:00 4 2 1 A R83 238 11:56 5 R R84 256 11:39 11:42 3 2 1 H W11 219 13:59 14:00 1 2 1 A W12 232 13:59 15:49 110 2 1 A W13 243 13:13 13:16 3 2 1 A W14 223 13:06 13:09 3 2 2 W15 220 14:05 14:29 24 1 1 H 9 8 W16 222 14:05 14:07 2 2 1 A W17 231 14:33 15:06 33 2 2 W18 257 14:14 14:20 6 2 1 H R65 230 14:31 14:33 2 2 1 A R68 232 14:13 14:16 3 2 1 H Controls W19 261 16:00 16:14 14 2 1 A W20 215 15:43 15:46 3 2 1 A W21 233 15:45 15:49 4 2 1 A W23 210 16:18 16:21 3 2 1 A W24 232 16:08 16:10 2 2 1 A W25 236 16:06 16:07 1 1 1 A W26 233 16:11 16:12 1 2 1 A W28 225 15:33 15:39 6 2 1 A W29 246 15:29 15:29 0 2 1 A W31 250 15:42 15:46 4 2 1 A W32 230 15:41 15:43 2 2 1 A W33 195 16:14 16:17 3 2 1 A W34 255 15:32 15:33 1 2 1 A W35 235 15:31 15:32 1 2 1 A W37 234 15:35 15:37 2 2 1 A W38 232 15:38 15:40 2 2 1 A W39 223 15:39 15:40 1 2 1 A W40 221 15:27 15:28 1 2 1 A W41 242 16:01 16:03 2 2 1 A W42 231 15:51 15:53 2 2 1 A W43 212 15:49 15:52 3 2 1 A W44 211 16:16 16:18 2 2 1 A W45 240 15:48 15:50 2 2 1 A W46 251 16:15 16:19 4 2 1 A

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Appendix C: Detailed Fish Injury and Survival Data

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Fish Date Condition ID Live/Dead Cause Injury Description Malady Severity Photo Treatment 1.3 ft Gate Opening 11/15/2017 1.3 Z79 dead 1 h shear torn left operculum yes major yes 11/15/2017 1.3 B99 dead 24 h shear LOE, torn left operculum yes major yes 11/15/2017 1.3 Z16 dead 24 h shear hemorrhaged right eye yes minor no 11/15/2017 1.3 Z44 dead 24 h unknown LOE, no obvious injuries yes minor no 11/15/2017 1.3 Z47 dead 24 h shear LOE, slight operculum tear yes minor no 11/15/2017 1.3 Z51 dead 24 h shear minor left eye hemorrhaged, LOE yes minor yes 11/15/2017 1.3 Z53 dead 24 h shear/mech. bruising on top of head, minor hem. left eye yes major no 11/15/2017 1.3 Z54 dead 24 h unknown LOE, no obvious injuries yes minor no 11/15/2017 1.3 Z93 dead 24 h shear/mech. hem., bulging left eye, bruising left side of head yes major yes 11/15/2017 1.3 Z57 dead 24 h shear major hem. left eye, torn left operculum, LOE yes major yes 11/15/2017 1.3 Z58 dead 24 h shear left operculum tear yes major yes 11/15/2017 1.3 Z62 dead 24 h unknown LOE yes minor no 11/15/2017 1.3 Z63 dead 24 h unknown LOE yes minor no 11/15/2017 1.3 Z69 dead 24 h shear right eye hem. yes major yes 11/15/2017 1.3 Z74 dead 24 h unknown LOE yes minor no 11/15/2017 1.3 Z83 dead 24 h unknown LOE yes minor no 11/15/2017 1.3 Z99 dead 24 h unknown LOE yes minor no 11/15/2017 1.3 Z26 dead 24 h unknown LOE, no obvious injuries external or internal yes minor no 11/15/2017 1.3 Z37 dead 24 h unknown LOE yes minor no 11/15/2017 1.3 S04 dead 24 h unknown no obvious injuries no no 11/15/2017 1.3 Z89 dead 24 h unknown no obvious injuries no no 11/15/2017 1.3 Z64 dead 24 h unknown no obvious injuries no no 11/15/2017 1.3 Z72 dead 24 h unknown LOE, no visible injuries yes minor no 11/15/2017 1.3 Z50 dead 24 h shear minor left eye hemorrhaged yes minor yes 11/15/2017 1.3 S08 dead 24 h shear hemorrhaged right eye yes major yes

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11/15/2017 1.3 Z40 dead 24 h unknown no visible injuries no no 11/15/2017 1.3 Z17 dead 24 h unknown tear at tag site no no 11/15/2017 1.3 Z90 dead 24 h unknown no obvious injuries no no 11/15/2017 1.3 Z88 dead 24 h unknown no obvious injuries no no 11/15/2017 1.3 Z33 dead 48 h shear right eye major hemorrhaged yes major yes 11/15/2017 1.3 Z39 dead 48 h shear left eye hemorrhaged yes minor no 11/15/2017 1.3 S05 dead 48 h shear hem., ruptured left eye yes major yes 11/15/2017 1.3 Z76 dead 48 h unknown no visible injuries no no 11/15/2017 1.3 S06 alive 48 h unknown LOE yes minor no 11/15/2017 1.3 32 alive 48 h unknown LOE, no obvious injuries yes minor no 11/15/2017 1.3 Z29 alive 48 h unknown LOE, no obvious injuries yes minor no 11/15/2017 1.3 Z35 alive 48 h unknown LOE, no obvious injuries yes minor no 11/15/2017 1.3 Z73 alive 48 h unknown LOE yes minor no 11/15/2017 1.3 Z20 alive 48 h unknown LOE yes minor no 11/15/2017 1.3 S07 alive 48 h unknown LOE yes minor no 11/15/2017 1.3 S02 alive 48 h unknown LOE yes minor no 11/15/2017 1.3 Z48 alive 48 h unknown LOE yes minor no 11/15/2017 1.3 S01 alive 48 h unknown LOE yes minor no 11/15/2017 1.3 Z92 alive 48 h unknown LOE yes minor no Control 11/15/2017 S12 dead 24 h hemorrhaged right eye yes minor no 11/15/2017 S23 dead 24 h no obvious injuries no no 11/15/2017 S24 dead 24 h no obvious injuries no no 11/15/2017 S20 dead 24 h no obvious injuries no no 11/15/2017 S19 dead 24 h no obvious injuries no no

Fish Date Condition ID Live/Dead Cause Injury Description Malady Severity Photo Treatment 1.3 ft Gate opening 11/16/2017 1.3 P00 dead 24 h unknown LOE yes minor no 11/16/2017 1.3 P01 dead 24 h unknown LOE yes minor no

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11/16/2017 1.3 P02 dead 24 h shear bulging/ruptured right eye yes major yes 11/16/2017 1.3 P05 dead 24 h unknown LOE yes minor no 11/16/2017 1.3 P09 dead 24 h unknown LOE yes minor no 11/16/2017 1.3 P13 dead 24 h shear torn right operculum yes major yes 11/16/2017 1.3 P11 dead 24 h unknown no visible injuries no no 11/16/2017 1.3 P14 dead 24 h unknown LOE, no visible injuries yes minor no 11/16/2017 1.3 P16 dead 24 h unknown no visible injuries no no 11/16/2017 1.3 P17 dead 24 h unknown LOE yes minor no 11/16/2017 1.3 P18 dead 24 h unknown LOE yes minor no 11/16/2017 1.3 P19 dead 24 h unknown LOE yes minor no 11/16/2017 1.3 S84 dead 24 h unknown LOE yes minor no 11/16/2017 1.3 S85 dead 24 h unknown no visible injuries no no 11/16/2017 1.3 S89 dead 24 h unknown LOE yes minor no 11/16/2017 1.3 S90 dead 24 h unknown LOE yes minor no 11/16/2017 1.3 S91 dead 24 h shear bent right operculum yes major no 11/16/2017 1.3 S92 dead 24 h mechanical LOE, scrape on nose yes major no 11/16/2017 1.3 S04 dead 24 h shear hemorrhaged left eye yes major yes 11/16/2017 1.3 S96 dead 24 h unknown no visible injuries no no 11/16/2017 1.3 S99 dead 24 h unknown LOE yes minor no 11/16/2017 1.3 P08 dead 24 h shear torn right operculum yes major yes 11/16/2017 1.3 P06 dead 48 h shear torn/bent right operculum yes major yes Control 11/16/2017 S62 dead 24 h unknown no visible injuries no no 11/16/2017 S47 dead 24 h unknown no visible injuries no no 11/16/2017 S42 dead 24 h unknown no visible injuries no no 11/16/2017 S33 dead 24 h unknown no visible injuries no no 11/16/2017 S67 dead 24 h unknown no visible injuries no no 11/16/2017 S73 dead 24 h unknown no visible injuries no no 11/16/2017 S77 dead 24 h unknown no visible injuries no no 11/16/2017 S79 dead 24 h unknown no visible injuries no no 11/16/2017 S38 dead 24 h unknown no visible injuries no no 11/16/2017 S30 dead 24 h unknown no visible injuries no no 11/16/2017 S29 dead 24 h unknown no visible injuries no no 11/16/2017 S63 dead 48 h unknown no visible injuries no no 11/16/2017 S44 dead 48 h unknown no visible injuries no no

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11/16/2017 S71 dead 48 h unknown no visible injuries no no 11/16/2017 S52 dead 48 h unknown no visible injuries no no 11/16/2017 S58 dead 24 h unknown LOE, no visible injuries yes minor no 11/16/2017 S54 dead 24 h unknown LOE, no visible injuries yes minor no 11/16/2017 S59 dead 24 h unknown LOE, no visible injuries yes minor no 11/16/2017 S65 dead 24 h unknown LOE, no visible injuries yes minor no 11/16/2017 S80 dead 24 h unknown LOE, no visible injuries yes minor no Fish Date Condition ID Live/Dead Cause Injury Description Malady Severity Photo Treatment 1.3 ft gate opening 11/17/2017 1.3 P60 dead 24 h shear LOE, bulging right eye, and slight bruising yes major yes 11/17/2017 1.3 P85 dead 24 h shear LOE, left eye hem. yes minor no 11/17/2017 1.3 P71 dead 24 h shear LOE, right operculum tear yes major no 11/17/2017 1.3 P98 dead 24 h shear torn right operculum yes major no 11/17/2017 1.3 R02 dead 24 h shear missing half of right operculum, hem. left eye yes major no 11/17/2017 1.3 R12 dead 24 h shear LOE, torn right operculum yes major no 11/17/2017 1.3 R13 dead 24 h shear hemorrhage left eye, torn left operculum yes major no 11/17/2017 1.3 P49 dead 24 h unknown LOE yes minor no 11/17/2017 1.3 P62 dead 24 h shear bulging left eye yes major no 11/17/2017 1.3 P66 dead 24 h unknown LOE, no obvious injuries yes minor no 11/17/2017 1.3 P74 dead 24 h shear LOE, torn right operculum, left eye bulging yes major no 11/17/2017 1.3 P80 dead 24 h shear LOE, minor left eye hem. yes minor no 11/17/2017 1.3 P43 dead 48 h shear minor left eye hem. yes minor no 11/17/2017 1.3 P39 dead 48 h shear torn right operculum yes major no 11/17/2017 1.3 P24 dead 48 h shear LOE, both eyes hemorrhaged yes major yes 11/17/2017 1.3 R22 dead 48 h shear hemorrhaged right eye yes major yes 11/17/2017 1.3 P69 dead 48 h shear LOE, major hem., left eye yes major no 11/17/2017 1.3 P75 dead 48 h shear minor left eye hem. yes minor yes 11/17/2017 1.3 R06 dead 48 h shear major bulging/hem. right eye yes major yes 11/17/2017 1.3 R09 dead 48 h shear LOE, torn right operculum yes major no 11/17/2017 1.3 P88 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 R08 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 R17 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 P57 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 P63 alive 48 h unknown LOE, no visible injuries yes minor no

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11/17/2017 1.3 P65 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 P70 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 P81 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 P82 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 P83 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 P84 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 P92 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 R14 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 P52 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 R15 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 R21 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 P28 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 P56 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 P40 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 P38 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 P32 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 P37 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 P95 alive 48 h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 P89 alive 48 h shear LOE, bulging left eye yes major no 11/17/2017 1.3 R10 alive 48 h shear torn right operculum, bulging right eye yes major no 11/17/2017 1.3 P44 alive 48 h shear hem./bulging/ruptured eye yes major no 11/17/2017 1.3 R04 alive 48h unknown LOE, no visible injuries yes minor no 11/17/2017 1.3 R00 alive 48h unknown LOE, no visible injuries yes minor no Control 11/17/2017 R31 alive 48 h shear hemorrhaged left eye yes major yes 11/17/2017 R34 alive 48 h shear minor right eye hemorrhaged yes minor yes 11/17/2017 R51 dead 24 h unknown no visible injuries no no 11/17/2017 R39 dead 24 h unknown no visible injuries no no 11/17/2017 R60 dead 24 h unknown no visible injuries no no Fish Date Condition ID Live/Dead Cause Injury Description Malady Severity Photo Treatment 2.0 ft gate opening 11/18/2017 2.0 R74 dead 1 h shear bulging left eye yes major yes 11/18/2017 2.0 R96 dead 1 h unknown no obvious injuries yes major no 11/18/2017 2.0 W14 dead 1 h unknown no obvious injuries yes major no

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11/18/2017 2.0 R71 dead 1 h unknown severe LOE yes major no 11/18/2017 2.0 W07 dead 24 h mechanical LOE, scale loss both sides yes major no 11/18/2017 2.0 W09 dead 24 h unknown LOE, no obvious injuries yes minor no 11/18/2017 2.0 W10 dead 24 h tag related tear at tag site no no torn right operculum, LOE, minor hem. right eye, flared 11/18/2017 2.0 W15 dead 24 h shear gills yes major no 11/18/2017 2.0 W18 dead 24 h unknown LOE yes minor no 11/18/2017 2.0 R68 dead 24 h unknown LOE yes minor no 11/18/2017 2.0 R70 dead 24 h unknown LOE yes minor no 11/18/2017 2.0 R77 dead 24 h unknown LOE yes minor no 11/18/2017 2.0 R80 dead 24 h unknown LOE yes minor no 11/18/2017 2.0 R84 dead 24 h unknown LOE yes minor no 11/18/2017 2.0 R86 dead 24 h unknown LOE yes minor no 11/18/2017 2.0 R88 dead 24 h unknown LOE yes minor no 11/18/2017 2.0 R99 dead 24 h shear LOE, minor hem. right eye yes minor no 11/18/2017 2.0 W04 dead 24 h unknown LOE yes minor no 11/18/2017 2.0 W13 dead 24 h unknown no visible injuries no no 11/18/2017 2.0 R82 dead 24 h unknown no visible injuries no no 11/18/2017 2.0 W02 dead 24 h shear bulging left eye, left operculum torn in half yes major yes 11/18/2017 2.0 W05 dead 24 h unknown LOE yes minor no 11/18/2017 2.0 R75 dead 48 h unknown no visible injuries no no 11/18/2017 2.0 R93 alive 48 h unknown LOE, no visible injuries yes minor no 11/18/2017 2.0 R92 alive 48 h unknown LOE, no visible injuries yes minor no 11/18/2017 2.0 R90 alive 48 h shear torn left operculum yes major yes 11/18/2017 2.0 R98 alive 48 h mechanical LOE, torn/crushed left operculum yes major no 11/18/2017 2.0 W01 alive 48 h unknown LOE, no visible injuries yes minor no 11/18/2017 2.0 R94 alive 48 h unknown LOE, no visible injuries yes minor no 11/18/2017 2.0 R73 alive 48 h unknown LOE, no visible injuries yes minor no 11/18/2017 2.0 R76 alive 48 h unknown LOE, no visible injuries yes minor no Control 11/18/2017 W26 dead 24 h unknown no visible injuries no no 11/18/2018 W21 alive 48 h shear Blown left pupil yes major yes 11/18/2018 W33 dead 48 h unknown no visible injuries no no

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Appendix D: Survival and Malady-free Outputs

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One hour survival for salmon passing through the RO at gate opening 1.3 and 2.0 ft at Cougar Dam, November 2017.

Control – 122 122 0 1.3 – 227 229 6 2.0 – 51 45 6 RESULTS FOR REDUCED MODEL (EQUAL LIVE/DEAD RECOVERY)

estim. std.err. S1 = 1.0 N/A Control group survival* Pa = Pd 0.9950 (0.0035) Recovery probability S2 = 0.9733 (0.0107) 1.3 ft survival S3 = 0.8824 (0.0451) 2.0 ft survival

* -- Because of constraints in the data set, this probability is assumed equal to 1.0; not estimated.

log-likelihood : -58.7297

Tau = 0.9733 (0.0107) 1.3 ft/Control ratio Tau = 0.8824 (0.0451) 2.0 ft/Control ratio

Z statistic for the equality of equal turbine survivals: 1.9618

Compare with quantiles of the normal distribution:

1-tailed 2-tailed For significance level 0.10: 1.2816 1.6449 For significance level 0.05: 1.6449 1.9600 For significance level 0.01: 2.3263 2.5758

Confidence intervals: 1.3 ft 2.0 ft 90 percent: (0.9557, 0.9910) (0.8081, 0.9566) 95 percent: (0.9523, 0.9944) (0.7939, 0.9708) 99 percent: (0.9457, 1.0010) (0.7662, 0.9985)

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Forty-eight hour survival for salmon passing through the RO at gate opening at1.3 and 2.0 ft, Cougar Dam, November 2017. Control – 122 released 91 alive 31 dead 1.3 – 227 released 146 alive 79 dead 2.0 – 51 released 26 alive 25 dead RESULTS FOR REDUCED MODEL (EQUAL LIVE/DEAD RECOVERY) estim. std.err.

S1 = 0.7459 (0.0394) {Control group survival Pa = Pd 0.9950 (0.0035) Recovery probability S2 = 0.6489 (0.0318) 1.3 ft survival S3 = 0.5098 (0.0700) 2.0 ft survival

* -- Because of constraints in the data set, this probability is assumed equal to 1.0; not estimated.

log-likelihood : -262.9107 Tau = 0.8699 (0.0627) 1.3 ft/Control ratio Tau = 0.6835 (0.1005) 2.0 ft/Control ratio

Z statistic for the equality of equal turbine survivals: 1.5735

Compare with quantiles of the normal distribution:

1-tailed 2-tailed For significance level 0.10: 1.2816 1.6449 For significance level 0.05: 1.6449 1.9600 For significance level 0.01: 2.3263 2.5758

Confidence intervals: 1.3 ft 2.0 ft 90 percent: (0.7668, 0.9731) (0.5181, 0.8489) 95 percent: (0.7470, 0.9929) (0.4864, 0.8805) 99 percent: (0.7084, 1.0314) (0.4246, 0.9424)

Likelihood ratio statistic for equality of recovery probabilities: 0.1511

Compare with quantiles of the chi-squared distribution with 1 d.f.:

For significance level 0.10: 2.706 For significance level 0.05: 3.841 For significance level 0.01: 6.635

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Injury-free rates for salmon passing through the RO at the 1.3 and 2.0 ft gate openings at Cougar Dam, November 2017.

Controls – 122 examined 118 without injuries 4 with injuries 1.3 ft – 220 examined 177 without injuries 43 with injuries 2.0 ft – 49 examined 42 without injuries 7 with injuries

RESULTS FOR REDUCED MODEL (EQUAL LIVE/DEAD RECOVERY)

estim. std.err. S1 = 0.9672 (0.0161) {Control group Injury-Free Pa = Pd 1.0 N/A Recovery probability* S2 = 0.8045 (0.0267) 1.3 ft Injury-Free S3 = 0.8571 (0.0500) 2.0 ft Injury-Free

* -- Because of constraints in the data set, this probability is assumed equal to 1.0; not estimated.

log-likelihood : -146.3883

Tau = 0.8318 (0.0309) 1.3 ft/Control ratio Tau = 0.8862 (0.0538) 2.0 ft/Control ratio

Z statistic for the equality of equal turbine survivals: 0.8769

Compare with quantiles of the normal distribution:

1-tailed 2-tailed For significance level 0.10: 1.2816 1.6449 For significance level 0.05: 1.6449 1.9600 For significance level 0.01: 2.3263 2.5758 Confidence intervals: 1.3 ft Tau 2.0 ft Tau 90 percent: (0.7809, 0.8827) (0.7978, 0.9746) 95 percent: (0.7712, 0.8924) (0.7808, 0.9916) 99 percent: (0.7522, 0.9114) (0.7478, 1.0246)

Likelihood ratio statistic for equality of recovery probabilities: -0.0001

Compare with quantiles of the chi-squared distribution with 1 d.f.:

For significance level 0.10: 2.706 For significance level 0.05: 3.841

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Malady-free rates for salmon passing through the RO at the 1.3 and 2.0 ft gate openings at Cougar Dam, November 2017. Controls – 122 examined 113 without maladies 9 with maladies

1.3 ft – 220 examined 117 without maladies 103 with maladies 2.0 ft – 49 examined 22 without maladies 27 with maladies

RESULTS FOR REDUCED MODEL (EQUAL LIVE/DEAD RECOVERY) estim. std.err. S1 = 0.9262 (0.0237) {Control group Malady-Free Pa = Pd 1.0 N/A Recovery probability* S2 = 0.5318 (0.0336) 1.3 ft Malady-Free S3 = 0.4490 (0.0711) 2.0 ft Malady-Free

* -- Because of constraints in the data set, this probability is assumed equal to 1.0; not estimated. log-likelihood : -217.8760

Tau = 0.5742 (0.0392) 1.3 ft/Control ratio Tau = 0.4847 (0.0777) 2.0 ft/Control ratio

Z statistic for the equality of equal turbine Malady- Free: 1.0277

Compare with quantiles of the normal distribution: 1-tailed 2-tailed For significance level 0.10: 1.2816 1.6449 For significance level 0.05: 1.6449 1.9600 For significance level 0.01: 2.3263 2.5758

Confidence intervals: 1.3 ft Tau 2.0 ft Tau 90 percent: (0.5097, 0.6386) (0.3569, 0.6126) 95 percent: (0.4974, 0.6510) (0.3324, 0.6370) 99 percent: (0.4733, 0.6750) (0.2846, 0.6848)

Likelihood ratio statistic for equality of recovery probabilities: 0

Compare with quantiles of the chi-squared distribution with 1 d.f.:

For significance level 0.10: 2.706 For significance level 0.05: 3.841 For significance level 0.01: 6.635

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Appendix E: Response to Agency Comments

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O

October 15, 2018

Fenton Khan

Environmental Resources Branch

US Army Corps of Engineers, Portland District 333 SW First Ave.

Portland, OR 97204

RE: ODFW review of two draft reports documenting fish injury and survival studies at Cougar Dam, 2017.

Dear Mr. Khan:

Thank-you for the opportunity to provide comments on the following two draft reports we received on September 13, 2018:

"Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon" August 2018 draft, prepared by Normandeau Associates, Inc. "Willamette Valley High Head Bypass Downstream Passage Prototype Evaluation: Sensor Fish Evaluation of the Regulating Outlet at Cougar Dam, 2017" September 2018 draft, prepared by Z.D. Deng, J.P. Duncan, J.J. Martinez, T. Fu. C.L. Grant, A. Salalila, and J.S. Cable of PNNL. ODFW has reviewed the draft reports and as few general comments provided below.

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The PPNL draft report references fish and wildlife habitat as a Willamette Project purpose in Section 1.0 Introduction, but then fails to list fish and wildlife habitat as a project purpose in Section 2.1 Study Site. Fish and wildlife habitat should be listed as a project purpose in Section 2.1 as well.

Also in the PNNL report, the location of Cougar Dam in Section 2.1 Study Site is described as “4 mi upstream of the confluence of the mainstem McKenzie River, at river kilometer 406 of the Willamette River.” The Willamette River kilometer is confusing as a reference point in this context.

Comment: ODFW supports more investigation of delayed mortality effects in the Normandeau study. The 25% mortality for control fish needs more attention for causality. In addition, ODFW would like to see the delayed mortality period extended to 72 hours if feasible. Response: The exact cause could not be determined. We added possible future actions in Section 5 (Considerations and Recommendations) to consider that may help address this issue in future studies. Principally we suggested securing test fish for two different hatcheries and tag a secondary control group of fish that would not be released into the river. Regarding 72h delayed assessment, Normandeau did extend some delayed assessments periods beyond 48 h earlier on in the conduct of HI-Z survival/injury studies. Generally most injured fish died within the first 24 h of passage thus the 48 h delayed passage assessment protocol has been in place for at least 20 years.

Comment: Also in the Normandeau study, the concern seems misplaced that one source of injury is the terminus of the induction system where fish fall into much faster RO water. Although this is a source of injury, it is a study effect due to study design. Under "natural" conditions, migrants in the forebay would volitionally enter the RO via the gates, and not be in a flexible hose attached to the side of the RO. A modification might be to try to eliminate the induction hose terminus as source of injury. This might be achieved by devising an induction point terminus upstream and near same depth as the RO entrance. Fish could still be tubed to this depth, but flow differentials (a source of injury) would be less. Response: Addressed much of this concern in Section 5.0. Considerations and Recommendations. The previous study conducted at the Cougar RO (Normandeau 2010) did release fish upstream of the flow control gates for the RO. However, the configuration of the control gates and the relatively small width of the gate openings appeared to contribute to observed injuries. Because of the temperature control tower upstream of the RO intakes deploying a hose that would reliably deliver tagged fish into the RO intake did not appear feasible.

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Comment: Neither study made any recommendations other than “more study” is needed. Given interest in volitional high head bypass as a possible way to move fish downstream, timely recommendations for managers to inform high head bypass are desired. Response: Recommendations were added to the report in Section 5.0.

Thanks again for the opportunity to comment. Please direct any questions or concerns regarding these comments to Kelly Reis ([email protected], 541-726-3515, x29) or Dave Jepsen ([email protected], 541-757-5148).

Sincerely,

Kelly Reis

Willamette Fish and Wildlife Policy and Program Manager

cc:Ian Chane, Rich Piaskowski, Brad Eppard, USACE Dan Spear, Christine Peterson, BPA Mike Hudson, USFWS Dave Jepsen, Jeff Ziller, ODFW Leslie Bach, Karl Weist, NWPCC Lawrence Schwabe, CTGRMelissa Jundt, Marc Liverman, Anne Mullan, Diana Dishman, NOAA

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October 17, 2018

Memorandum – delivered via email

To: Fenton Khan, Environmental Resources Branch Portland District, US Army Corps of Engineers (Corps)

From: Diana Dishman, Willamette Branch West Coast Region, National Marine Fisheries Service (NMFS)

Subject: NMFS’ review of two draft reports regarding high head bypass at

Cougar Dam Regulating Outlet Thank you for the opportunity to review the following reports which we received September 13, 2018:

 “Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon” August 2018 draft, prepared by Normandeau Associates, Inc.  “Willamette Valley High Head Bypass Downstream Passage Prototype Evaluation: Sensor Fish Evaluation of the Regulating Outlet at Cougar Dam, 2017” September 2018 draft, prepared by Z.D. Deng, J.P. Duncan, J.J. Martinez, T. Fu, C.L. Grant, A. Salalila, and J.S. Cable of PNNL this memo summarizes comments prepared by NMFS’ Willamette Branch technical staff. A few general comments are provided, followed by detailed comments.

General Comments

Both reports are clearly written with excellent graphics and tables. We appreciate the opportunity to review both reports at once because it enables clearer comparison of results from the different methods.

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We recommend further study of alternative configurations of bypass pipes at Cougar dam. Configurations that minimize the velocity change impacts observed at the transition from the induction system to the RO tube and at the entrance to the stilling basin would reduce the most likely sources of injury identified in these studies, and could provide safer high-head passage routes for fish.

Specific Comments

Biological Fish Injury and Survival Evaluation

1. Comment: What are possible causes of the high levels of control fish mortality? Response: The exact cause could not be determined. We added possible future actions in Section 5: (Considerations and Recommendations) to consider that may help address this issue in future studies. Principally we suggested securing test fish for two different hatcheries and tag a secondary control group of fish that would not be released into the river.

2. Comment: “The release hose/pipe was continuously supplied with river water to ensure fish were transported quickly to the desired release point.” Please provide an estimate of the flow (cfs) and depth of water in the 4” pipe. Response: Information provided in report.

3. Comment: How are the unexplained mortalities (of control and injury-free test fish) being further investigated, and when will we have the results of those investigations? Response: See response to comment #1. Presently no specific tests are being planned to seek out cause.

4. Comment: Please include 48-hour survival rates from prior Cougar RO studies (2009) with results presented in this study for comparison. Response: Information added in Section 4.0 Discussion

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Biological Fish Injury and Survival Evaluation at the Regulating Outlet of Cougar Dam, Oregon

Sensor Fish Evaluation

1. Comment: "Please provide here or elsewhere more information about the cause of the time constraints that affected both studies. Normandeau Response: Because of the time and operational constraints a reduced sample size of juvenile Chinook Salmon was released for the 2.0 ft gate opening tests. The study was delayed because of Cougar turbine unit maintenance. We had to wait until the turbine work was complete before we were able to conduct the test. Once the turbine maintenance was complete, we were given a short window to conduct the RO test before the turbine maintenance team had to test the turbine, which was schedule for several weeks. Therefore, the USACE personnel had to reduce the number of fish for the 2.0 ft gate opening and cancel the 1.7 ft gate opening test in order to be able to conduct the test in a short timeframe. 2. Comment: Comparisons to previous studies of passage through the Cougar RO are very useful. Can traces from sensor fish in those studies be compared to these results? It would be very useful to see if any part of the impact profile other than the transition from the bypass pipe to the RO tube was different between the 2009 Cougar RO passage results and this study.

3. Comment: The first two paragraphs of the Discussion section seem unnecessary, and are redundant with the introduction.

Please direct questions or concerns about these comments to me at [email protected] or 503- 736-4466. cc: Fenton Khan, USACE Christine Peterson, BPA Mike Hudson, USFWS Kelly Reis, David Jepson, ODFW Leslie Bach, NWPCC Lawrence Schwabe, CTGR Anne Mullan, Lance Kruzic, NMFS-WCR

Jim Myers, NWFSC

70 Normandeau Associates, Inc.