B01__Draft_PWS_Klamath_FAR_Compilation_Report_1.pdf

Version: 10/11/2024

Draft PERFORMANCE WORK STATEMENT (PWS)

Synthesizing Information to Improve Understanding of the Need, Design, and

Performance of Flow Augmentations to the Lower Klamath River

I. Background and History:

The U.S. Fish and Wildlife Service (2003) estimated that at least 34,000 adult salmon prematurely perished in the Lower Klamath River in late summer of 2002. This mass mortality event was the first of its kind in modern Klamath River basin history. The impact of this event was significant to public and tribal interests that rely on the Klamath Basin fisheries as a cultural and economic resource. The event stimulated considerable interest to uncover the reasons why it happened and what actions could be implemented to avoid a similar die-off in the future.

Immediately following the 2002 die-off event, the USFWS (2003b), the Yurok Tribe

(Belchik et al., 2004) and the CDFW (2003) completed reports aimed at better understanding the impacts and the potential causes of the event. Upon review of the available physical, chemical, and biological data, these reports concluded that a combination of a relatively large run of adult salmon, warm water temperatures, and low river flows caused crowding that resulted in small areas for suitable holding habitat and thus stressful holding conditions that promoted a rapid proliferation of the fish diseases Ichthyophthirius multifiliis (Ich) and

Flavobacter columnare (Columnaris) that caused the observed mass mortality. The reports further concluded that increases in Lower Klamath River flows from regulated upstream sources was the most viable and controllable option to avert a similar event in the future. The use of water from Lewiston Dam on the Trinity River was deemed the most influential to avert a disease outbreak in summer in the Lower Klamath River because of its unique ability to reduce water temperatures in the Lower Klamath River at higher flows (Reclamation 2017).

Since the 2002 die-off event, flow augmentation releases (FARs) from Lewiston Dam have been used ten times to improve environmental conditions in the Lower Klamath River

(Figure 1). The average volume of water used in the events is around 31,000 acre-feet.

Figure 1. Flow augmentation releases from Lewiston Dam used to protect adult salmon in the

Lower Klamath River since 2002.

In each year of implementation, FARs were directed by the U.S. Bureau of Reclamation

(hereafter, Reclamation) following a National Environmental Policy Act review that incorporated the best available information and input from a Technical Team comprised of biologists and disease experts from State, Federal, and Tribal entities in the basin.

Environmental assessments were completed in 2003, 2004, 2008, 2009, 2012, 2013, 2015, and

2016 resulted in Findings of No Significant Impacts and implementation in all years except

2008 and 2009. In 2008 and 2009, FARs were not formally implemented because hydrological conditions in the lower Klamath River were deemed adequate for Chinook salmon in the summer migration period. In 2014, Reclamation did not complete a NEPA review of that year’s

FAR proposal but used the emergency procedures of the Council on Environmental Quality following implementation of the FAR action.

In anticipation of the need to implement FARs into the future without the requirement of annual environmental reviews, Reclamation completed an Environmental Impact Statement for the Long-Term Plan for Protecting Late-Summer Adult Salmon in the Lower Klamath River and signed a Record of Decision (ROD) (Reclamation 2017). Since 2017, the ROD has served as the principal basis for implementing protective flows for the Lower Klamath River during the late summer and early fall in 2018, 2020, and 2022.

The Proposed Action in the ROD (Reclamation 2017) is comprised of three flow augmentation components to be implemented as needed in a phased approach, based on environmental (e.g., flow) and biological conditions. The three components include: (1) a preventive base-flow release from Lewiston Dam that targets increasing the base flow of the

Lower Klamath River at the Klamath gage (USGS gage #11530500) to 2,800 cubic feet per second (cfs) from mid-August to late September to improve environmental conditions for salmon; (2) a one-day preventive pulse flow (targeting 5,000 cfs at the Klamath gage) to alleviate continued poor environmental conditions and signs of Ich infection on adult salmon in the Lower Klamath River; and (3) a five-day emergency pulse flow (targeting 5,000 cfs at the

Klamath gage) to be used on an emergency basis to avoid a significant die-off of adult salmon when the first two components of the Proposed Action do not meet their objectives. In recognition that there was much to still learn, the Proposed Action incorporated an adaptive management approach that is flexible and responsive to real-time environmental (e.g., flow, water temperature, weather) and biological monitoring information to determine when to implement any one or a combination of these actions. In addition, the proposed action incorporated the continued use of a Technical Team, comprised of state and federal agency and tribal staff biologists, to assist Reclamation in its FARs decisions. Since 2017, only the first component of the Proposed Action has been implemented.

Flow pulses from Lewiston Dam and Iron Gate Dam that occur during the period of interest (August 15 to the end of September) for other reasons are also incorporated into the decision framework by Reclamation for implementing FARs. For example, changes to hydrology to the lower Klamath River that result from scheduled ceremonial flows for downstream native American Indian tribes are also important considerations (as is realtime monitoring information on infection prevalence of adult salmon, etc.) that are accounted for when determining when and if a formal FARs is needed in any year. In odd years, the Hoopa

Valley Tribe typically requests a pulse flow from Lewiston Dam to arrive at the Hoopa

Reservation in time for their Ceremony, usually late August or early September. This pulse flow, including the Trinity River Restoration Program approved ramp-up and down rates, usually lasts about 8 days and the peak may exceed 2300 cfs. The peak flow represents over a five-fold increase over the typical late summer flow of 450 cfs released at Lewiston Dam. This pulse flow results in a substantial flow increase and water temperature reduction throughout the

Trinity River and to some extent even in the lower Klamath River. In contrast, the Yurok Tribal

Dance flows that have historically originated from releases from Iron Gate Dam occur in even years and also in late August or early September. The Yurok Ceremonial flows typically also exhibit a one-day peak (about 1900 cfs) and when factoring in the ramping up and down from this peak it lasts between 5 to 7 days. This peak flow represents about a two-fold increase from the base flow (typically 900 cfs) for this time of the year and also has a strong but short influence on the flow in the lower Klamath River. Unlike the releases from Lewiston Dam that are cold, the flows from Iron Gate Dam have been relatively warm and so the effects to the lower Klamath River are limited to an increase in flow in the lower Klamath River.

In yet another example, Reclamation, in coordination with the Technical Team used a short-term pulse from Lewiston Dam on the Trinity River in July 2021 to stimulate upstream movement of adult spring run salmon from the Lower Trinity River that were exhibiting signs of Columnaris infection and stress (Reclamation 2021). Although no formal study was undertaken to evaluate the effects of the pulse flow, underwater direct observation by federal, state, and Tribal fishery biologist confirmed the fish actively moved (presumably upstream) and dispersed in response to the pulse, suggesting it was successful in meeting the goal of spreading these fish out. This pulse flow was considered by many on the Technical Team to have been a success and a preemptive flow action that lowered the potential need for a larger flow action in the typical action window of mid-August to late September, as prescribed by the 2017 ROD.

With more than two decades of involvement, the Technical Team gained considerable experience with Ich infection dynamics and the role of FARs in reducing prevalence of this disease. Perhaps the most notable experiences occurred in 2014, 2015, and 2022 when FARs were triggered because adult salmon in the Lower Klamath River were experiencing increasing severity of Ich infections (>30 trophonts per gill arch) during the summer, yet they did not prematurely die as conceptual models had predicted. This suggests the FARs may have been effective at meeting their intended goals but for reasons that are unclear.

The removal of four dams on the Klamath River in 2024 is altering the environmental setting of the Klamath River. Flow, water temperature, water quality and sediment transport and deposition in downstream locations have all been altered with removal of the dams. The most notable changes to these variables are occurring at the areas of dam removal with progressively less pronounced effects occurring downstream. Additionally, it is anticipated that the influence of sediment transport and deposition to the downstream aquatic environment will lessen with time (Reclamation 2012, KRRC 2022).

In September 2024, the FARs Technical Team considered the effects of dam removal on turbidity and possible implications to disease risk to immigrating adult Chinook salmon of the lower Klamath River. Ultimately, this close review of water quality impacts by the Technical

Team and field observations of on infection status of adult salmon did not reveal any threat and no FARs action was implemented (USBR 2024). However, concerns remain regarding the potential effects from increased fine sediment deposition, and possible attendant water quality changes, that may affect Ich and Columnaris infections to adult chinook salmon of the lower

Klamath River, at least in the short-term.

The objective of this synthesis study is to improve the understanding of fish disease dynamics through analysis of relationships (correlations) between physical, chemical, and biological variables and fish infection and disease dynamics in the Lower Klamath River.

While not all changes to Lower Klamath River conditions from dam removal are yet known, this synthesis will improve the understanding of disease patterns and conditions prior to removal and could enable informed hypotheses for patterns following dam removal.

II. Scope and Purpose:

Reclamation seeks professional services to conduct a detailed review of the environmental effects to Ich and Columnaris prevalence in the lower Klamath River that are influential to the decision framework for implementing FARs to the Lower Klamath River. The review will explore relationships of environmental variables with the fish disease information observed from 2002 until Klamath Dam removal in 2024. The outcome will help inform management actions to more effectively reduce the occurrence of fish diseases in the Lower

Klamath River. The review will also create a data-supported conceptual model on how environmental factors (physical, biological, or chemical) influence Ich and Columnaris infections that lead to premature mortality of adult salmon in the Lower Klamath River. The conceptual model is anticipated to direct future research and monitoring needs to ensure resource protection and prudent use of water.

III. Benefits:

This project will improve understanding of the environmental variables affecting Ich and

Columnaris outbreaks that have occurred in the Lower Klamath River. In turn, this will help focus research and management aimed at protecting adult salmon in the Klamath River basin while ensuring water resources for such protections are prudently used. The project will positively benefit salmon populations and accrue to the environment, public, and Tribal entities by way of improved environmental benefits of salmon returns, better fishing opportunities, and strong cultural connection to the fishery into the future.

IV. Type of Contract

The government anticipates awarding a firm fixed price type task order.

V. Period of Performance

The period of performance for this task order shall be 18 months from Award Date.

VI. Performance Work Statement

The contractor shall provide the personnel (including a project manager, biologists, environmental scientists, etc.), materials, and travel (as needed) to complete the project Tasks.

The consultant understands that only the Contracting Officer (CO) has the authority to make changes to this Agreement. The principal scope of work to be performed by the contractor will consist of the following Tasks:

A. Task 1 – Review Documents

Since 2002, monitoring and associated documentation of adult salmon and disease prevention in the Lower Klamath River have been extensive. The successful contractor will review at a minimum the following documents:

a) Asarian, J. E., K. De Juilio, S. Naman, D. Gaeuman, and T. Buxton. 2023. Synthesizing

87 years of scientific inquiry into Trinity River water temperatures. Report for the

Trinity River Restoration Program (TRRP). Riverbend Sciences, Eureka, California. To become familiar with the databases. (https://www.trrp.net/library/document?id=2615 )

b) Belchik, M., D. Hillemeier, R. Pierce. The Klamath River Fish Kill of 2002, Analysis of

Contributing Factors. Yurok Tribal Fisheries Program. 42 pp.

https://www.yuroktribe.org/_files/ugd/23c897_4fc423f3137641e6954547aa7436badf.pdf

c) Bureau of Reclamation. 2017. Long Term Plan to protect adult salmon EIS/ROD.

Various sections (Executive Summary, Draft EIS, Chapters 1 – 4) https://www.usbr.gov/mp/nepa/nepa_project_details.php?Project_ID=22021

d) Bureau of Reclamation. 2016. Long Term Plan to Protect Adult Salmon in the Lower

Klamath River, Independent Scientific Peer Review, October 2016. 492 pp.

https://www.trrp.net/library/document?id=2615 https://www.yuroktribe.org/_files/ugd/23c897_4fc423f3137641e6954547aa7436badf.pdf https://www.usbr.gov/main/qoi/docs/Independent_Scientific_Review_Protecting_Adult_

Salmon_Full.pdf

e) Bureau of Reclamation. 2021. Environmental Assessment EA-21-19-NCAO, 2021

Trinity River Summer Flow Augmentation from Lewiston Dam 35 pp.

https://www.usbr.gov/mp/nepa/includes/documentShow.php?Doc_ID=50228

f) California Department of Fish and Wildlife. 2004. September 2002 Klamath River Fish-

Kill: Final Analysis of Contributing Factors and Impacts. July 2004. Northern

California –North Coast Region. 183 pp, (https://www.trrp.net/library/document/?id=298)

g) National Marine Fisheries Service and U.S. Fish and Wildlife Service. 2013.

Memorandum from Irma Lagomarsino (NOAA) and Nickolas Hetrick (USFWS) to Brian

Person, Reclamation Northern California Area Manager. Subject 2013: Fall Flow

Release Recommendation. 46 pp. (comm)

h) U.S. Fish and Wildlife Service. 2002. Klamath River Fish Die-off, September 2002.

Mortality Report. Arcata Fish and Wildlife Office, Arcata, CA. 35pp.

( https://www.trrp.net/library/document/?id=301 )

i) U.S. Fish and Wildlife Service. 2003. Klamath River Fish Die-off, September 2002.

Causative Factors of Mortality Report. Arcata Fish and Wildlife Office, Arcata, CA.

128pp. ( https://www.trrp.net/library/document/?id=302 )

B. Task 2 - Flow Analysis and Reporting

Klamath River flows at Klamath near the Pacific Ocean are a major factor when considering the use of FARs to improve environmental conditions for adult Chinook salmon in the Lower Klamath River. River flows at this location in the basin result from the hydrologic https://www.usbr.gov/main/qoi/docs/Independent_Scientific_Review_Protecting_Adult_Salmon_Full.pdf https://www.usbr.gov/main/qoi/docs/Independent_Scientific_Review_Protecting_Adult_Salmon_Full.pdf https://www.usbr.gov/mp/nepa/includes/documentShow.php?Doc_ID=50228 https://www.trrp.net/library/document/?id=298 https://www.trrp.net/library/document/?id=301 behaviors of the watershed, which makes an analysis and reporting on surface flows at several gages in the Klamath River basin a foundational area of the synthesis report. Information generated from this task will be used in further analyses in Tasks 3 and 6.

The contractor shall update an existing database of gaged surface flows in the Klamath

River basin. This database will be based on a common database program accessible to most

(e.g., Excel) and address the following:

a) The database will incorporate the highest resolution and “approved” daily average flow data from U.S. Geological Survey (USGS) records for gages on the

Trinity River at Lewiston (USGS gage number (#) 11525500) and Hoopa

(#11530000) and for the mainstem Klamath River at Iron Gate (#11516530), Orleans

(#11523000), and Klamath (#11530500). The database will include data for the period of record (POR) for the months of June through October 2024. Periods of missing data will be filled by using USGS methods or other industry approved methods.

b) Calculate the daily average, 7-day average (June 1 to October 26) and average monthly flow for each gage for June thru October for the POR.

c) Create an exceedance probability plot and table for each gage to characterize each

7-day period and each month across the POR.

d) Describe any temporal trends in the dataset at either the 7-day average or monthly scales over the POR. Use graphics to depict the trends.

e) Compare 2002 (the year of the fish die-off) to 2014, 2015, 2022, and the POR at the

7-day average and monthly scales from June through October. Use graphics to depict these comparisons.

f) Create a table with details on the timing, frequency, magnitude, and volume of each

FAR (from Lewiston Dam) and Tribal Dance flow (from Lewiston for Hoopa

Ceremonial flows and the Iron Gate gage for Yurok ceremonial flows), over the POR.

C. Task 3 - Water Temperature Data Analysis and Reporting

Water temperatures affect and can even control the distribution and survival of salmon and the dynamics of fish pathogens in a river. As such, a contemporary analysis and report of water temperatures in the Klamath River basin will serve as one of the foundational areas of the document and will be important to subsequent analyses as identified in Task 6. Address the following:

a) Update the existing database created by Asarian et al. (2023) to include water temperature data through October 2024 for gages identified in Task 2. Only

“approved” USGS daily data or data that has undergone a similar level of quality control review will be used to fill in missing data as needed to complete the POR.

b) Calculate the average daily, 7-day average, 7-day average daily maximum, and average monthly water temperatures from June 1 through October for the POR.

c) Create exceedance probability plots for 7-day average, 7-day average daily maximum, and average monthly water temperatures (June through October) over the POR.

d) Assess if water temperatures, as defined by the 7-day average, 7-day average daily maximum, and average monthly water temperatures are static or show a trend of warming or cooling in the POR at each gage.

e) Compare the average daily, 7-day average, 7-day average daily maximum, and average monthly water temperatures from 2002, 2014, 2015, and 2022 to the

POR and then for 2003 through 2024.

f) Identify any associations of the 7-day average, 7-day average daily maximum, and average monthly water temperatures with the and 7-day average and monthly flow information from Task 2. Conduct this review for the Orleans, Hoopa, and Klamath at Klamath gages.

g) Describe the spatial and temporal influence of the FARs and Tribal dance flows from Lewiston Dam and Iron Gate Dam on the daily average temperatures at the

Hoopa, Orleans and Klamath gage over the POR.

D. Task 4 - Meteorology & Lunar Data Analysis and Reporting

Meteorology may have a direct or indirect influence on salmon immigration behavior.

Similarly, lunar cycles are important to circadian rhythms and may influence immigration of salmon. Address the following:

a) Obtain and organize in the database the data for the following information:

solar radiation data, air temperature data, barometric pressure, a metric for wildland fire smoke (e.g. air quality index), and lunar cycle information. Use similar sources as were used in Asarian et al (2023). Only include data from

June 1 through October for 2002 to present.

b) Calculate daily average,7-day average and monthly average values for each of the above variables, as appropriate, for the regions near or at the towns of

Klamath, Orleans, and Hoopa.

c) Analyze and describe the relationships of the meteorological variables and lunar phases to adult chinook salmon immigration information (See Task 6).

E. Task 5 - Water Chemistry Data Analysis and Reporting

Water chemistry is an important element of the environment of aquatic organisms.

Water chemistry information will be assessed and reported on to identify if certain constituents may have exceeded criteria considered stressful to adult Chinook salmon. Information generated from this task will also be used in subsequent analyses in Task 6. Address the following:

a) Create or update an existing database with water quality data for the Klamath

River at Orleans and Klamath and the Trinity River at Hoopa for 2002 through

2024. This data will include organic/ inorganic water sample results, as well as basic information on water chemistry (dissolved oxygen, total suspended solids or turbidity, specific conductance, pH, algae concentrations) for the June through October period. Sources are likely to include routine and synoptic survey results collected by the Yurok Tribe (Environmental Department | Yurok

Tribe), the Karuk Tribe ( https://waterquality.karuk.us/), the Hoopa Valley Tribe

(hoopatepa.org), and the Regional Water Quality Control Board. These data may be contained within the Federal Water Quality Portal

(https://www.waterqualitydata.us/ ), and the California Environmental Data

Exchange Network (http://www.ceden.org/). Additional monitoring results from https://doimspp-my.sharepoint.com/personal/pzedonis_usbr_gov/Documents/Documents/New%20folder/Environmental%20Department%20|%20Yurok%20Tribe https://doimspp-my.sharepoint.com/personal/pzedonis_usbr_gov/Documents/Documents/New%20folder/Environmental%20Department%20|%20Yurok%20Tribe https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwaterquality.karuk.us%2F&data=05%7C02%7Cpzedonis%40usbr.gov%7C998e6a97ed0b44b5387e08dc16d89d93%7C0693b5ba4b184d7b9341f32f400a5494%7C0%7C0%7C638410366812039583%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=kyP0lGUwSONZj67PAfdxR%2FjygfBatBjh5PiL7UzBrgE%3D&reserved=0 http://www.hoopatepa.org/water.html http://www.hoopatepa.org/water.html https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.waterqualitydata.us%2F&data=05%7C02%7Cpzedonis%40usbr.gov%7C998e6a97ed0b44b5387e08dc16d89d93%7C0693b5ba4b184d7b9341f32f400a5494%7C0%7C0%7C638410366812026235%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=KE6urZ3lpAPuLGoywhy8vQ0fVLPoht3GLG5pstHn294%3D&reserved=0 https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.waterqualitydata.us%2F&data=05%7C02%7Cpzedonis%40usbr.gov%7C998e6a97ed0b44b5387e08dc16d89d93%7C0693b5ba4b184d7b9341f32f400a5494%7C0%7C0%7C638410366812026235%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=KE6urZ3lpAPuLGoywhy8vQ0fVLPoht3GLG5pstHn294%3D&reserved=0 https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ceden.org%2F&data=05%7C02%7Cpzedonis%40usbr.gov%7C998e6a97ed0b44b5387e08dc16d89d93%7C0693b5ba4b184d7b9341f32f400a5494%7C0%7C0%7C638410366812033430%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=gumdR4zaO4xu54i%2Fv6p7O2F0b3PKBtZpoqfdIFkV1i8%3D&reserved=0 other sources may be included if they’ve been subjected to quality control and come from a reputable source.

b) Create a table that reflects contemporary EPA threshold criteria for harm to adult salmon for each chemical identified from part “a”, above.

c) Document the relationships of the water chemistry data to the aquatic life criteria of part “b” (above).

F. Task 6 - Biological Data Analysis and Reporting

This task includes obtaining and organizing biological monitoring data collected from

2002 to 2024 in support of annual reviews of the need for a FAR action. Address the following:

1. Estuary and River Entry by Adult Chinook Salmon:

a) Hold up to eight 1-hr meetings with staff of the California Department of Fish and Wildlife, Hoopa, Yurok and Karuk Tribes to obtain information to assess the spatial and temporal distribution of spring- run and fall -run salmon from the estuary to upriver locations from June through October from 2002 through 2024.

(Information will include, but is not limited to, pre- and post-season run size estimates, temporal and spatial sport and tribal harvest data, any weir count information, fish density information in the river (e.g., Yurok Tribal Sonar studies or snorkel data) or fish use in thermal refugia. (Also See NOAA and

USFWS 2013).

b) Organize information from “a” in a spreadsheet in chronological and spatial order. Separate the spring run and fall run chinook where coded wire tagging, or genetic data allow.

c) Calculate average and median dates for initial and peak entry into the estuary, upriver weir locations, and the hatcheries in the Klamath River basin 2002 to through 2024. Include data for tributaries if available (e.g., Shasta River).

d) Create plots of cumulative entry by time and daily entry by date. Include in these plots the median dates for initial and peak entry into the estuary and at up weir locations.

e) Describe the historic (pre-dam and pre hatchery) run timing of adult Chinook salmon races into the Klamath River estuary and in the lower Klamath River below Weitchpec. Use historic literature (e.g., Snyder 1931, Moffett and Smith

1950, NRC 2004, etc.), and any cannery records, if available.

f) Optional Subtask: If records exist from “e” above, describe any differences in the run timing of the different salmon races to the estuary/lower Klamath River before and after the dams and hatcheries were built.

g) Assess through graphical review (and statistical analyses, if possible), the relationship of fish movement into the estuary and above to flow (Task 2), water temperature (Task 3), meteorology and lunar phase (Task 4), and water chemistry (Task 5). This assessment will only include data from 2002 to 2024.

2. Genetics and Run Timing of Adult Salmon

a) The contractor will acquire the services of 3 fish genetics experts on the run timing of different races of adult chinook salmon on the west coast.

b) The contractor will chronical spring-run and fall run chinook salmon mating protocols at Iron Gate and Trinity River hatcheries (operated by the State of

California) since the hatcheries were built.

c) The genetics experts will assess and report on the plausibility that the adult

Chinook Salmon stocks of the Klamath River basin includes an intermediary run of fish (early to mid- summer) that would otherwise not exist absent the dams and/or hatcheries. This review will include, but is not limited to, findings of contemporary peer-reviewed literature on genetics and how they influence immigration of chinook salmon (focus on the Klamath River basin), any historic account information (Task 6.1), and mating protocol reviews (Task 6.2b).

d) Evaluate the potential implications of altered run timing of adult salmon to disease epizootics in the lower Klamath River.

3. Pathogen Infection Data Compilation and Review

a) The contractor, in collaboration with Reclamation, will hold up to six 1-hr online meetings with staff from the Hoopa, Yurok, and Karuk Tribes, Oregon State

University, the California Department of Fish and Wildlife, and the U.S. Fish and Wildlife Service to define and acquire all applicable Ich/Columnaris related information.

b) Contractor will organize all Ich/Columnaris infection information chronologically and spatially in a spreadsheet for the entire Klamath River basin for 2002 through 2024.

c) Contractor will assess and report on the relationships of pathogen infection data

(through graphical review, and statistical analyses, if possible) to flow (Task 2), water temperature (Task 3), lunar cycle (Task 4), water chemistry (Task 5), and fish movement (Task 6.1 and 6.2) over the period of 2002 to 2024.

4. Pre-spawn Mortality Review

a) Contractor is to obtain data from the USFWS, Arcata, CA on pre-spawning mortality estimates for the spring and fall run chinook salmon in the Trinity

River and the Klamath River from 2002 to 2024.

b) Assess inter- and interannual trends of pre spawn mortality of adult chinook salmon in the Klamath River basin to Ich/Columnaris infectivity severity in the, as identified in subtask “a” above.

G. Task 7 - Influences of the Removal of Klamath River Dams

In 2024, the removal of 4 dams in the upper Klamath River Basin altered the sediment and water characteristics below the dam removal sites including the lower Klamath River.

Some of these changes will be temporary in nature (e.g., high turbidity from dam removal activities) that lessen over time and with distance below the dams, while other water quality parameters (water temperature, nutrient concentrations, etc.) will represent a new and resilient condition simply because the river water will no longer pass through reservoirs that alters its physical and chemical properties. The Klamath River Renewal Corporation (KRRC, 2022

(page 3-20)), states the following:

Most of the 1.5 to 2.4 million tons of sediment released from the reservoirs (table 3.1-3) are expected to be transported to the Pacific Ocean over a relatively short period (i.e., within six months of drawdown) because of relatively high-flow rates in the river during this period and the mostly fine-grained nature of the sediment. Temporary sediment deposition in slack-water areas (such as pools, eddies, backwater channel) would be likely, but deposits are expected to be remobilized during higher flows.

Because the dam removals will have some short term and possibly some longer-term influence on sediment and water quality dynamics of the lower Klamath River, address the following:

Using the best available information, and consulting with fish disease experts, provide a narrative assessment of the possible implications of changes in sediment composition (and nutrients), turbidity, flow, and water temperature, to future Ich and Columnaris infections in adult salmon in the Lower Klamath River.

H. Task 8 - Flow Management & Trigger Criteria Review

a) Chronical the application of fish disease information, environmental data, flow trigger criteria, and flow management used for the Lower Klamath River since

2002. (See Reclamation 2016, Reclamation 2017, Reclamation 2021 and formal notes made by Reclamation at all calls with the Technical Team members from

July through October of 2017 through 2024).

I. Task 9 – Draft Report Review

a) Following completion of the draft report for Tasks 2 - 8, the contractor, in coordination with Reclamation, will submit the report to the Technical Team members for their technical review.

b) The Contractor, in coordination with Reclamation, will organize and consolidate substantive comments and generate a response to comments document.

c) The Contractor will host an online meeting with the Technical Team and the fish disease and genetics experts to share the comments and responses of this first draft report.

J. Task 10 – Workshop: Conceptual Model Development and

Recommendations

Conceptual models can help synthesize and interpret complex data sets thereby aiding managers in making inferences about possible consequences of management strategies. A conceptual model is needed to identify key ecosystem/fish disease (Ich/Columnaris or others) relationships of the Lower Klamath River to expose critical uncertainties, identify opportunities for efficient and meaningful monitoring and research, and define priority management questions. Address the following:

a) The contractor in collaboration with Reclamation and fish disease and genetics experts, will use information from the draft report and any other pertinent information, to construct draft conceptual model(s), identify critical uncertainties, develop a draft monitoring and research plan, and define priority management actions.

b) The contractor will collaborate with Reclamation to define the agenda, logistics, and the anticipated outcomes for the 1-day in-person workshop to be attended by representatives of the Technical Team, fish disease experts, and the geneticists to critique and improve the conceptual model.

c) Prior to the workshop and based on newly acquired information from Tasks 2-8, the contractor will conduct a critical review of the existing three-tiered flow criteria of the ROD for implementing FARs, the underpinning reasons for each, and draft a set of new recommendations if applicable.

d) In coordination with Reclamation, the contractor will lead the in-person workshop at the Reclamation Office in Weaverville, CA.

e) The participation by the disease/genetics experts will be compensated by the contractor and will be required to read materials identified in Task 1 and read the draft report for Tasks 2-8 prior to the workshop.

f) The contractor, in coordination with Reclamation, will update the draft report

(now called Second Draft) reflecting input from the workshop.

g) The contractor, in coordination with Reclamation, will lead and host an online meeting with members of the Technical Team/disease and genetics experts to inform them of any significant changes in contents to the Second Draft report.

h) The contractor, in collaboration with Reclamation, will finalize the Second Draft report following Peer Review (Task 11).

K. Task 11 - Peer Review

After finalization of the Second Draft report, it will be Reclamation’s sole responsibility to conduct a Peer Review of the document before the contractor can proceed to finalization of the report. The Office of Management and Budget requires that influential scientific information of highly influential scientific assessments be peer reviewed by qualified specialists before it’s disseminated by the Federal government.

a) Reclamation will oversee the Peer Review process of the second draft, including the selection of the peer reviewers in accordance with the Office of Management and Budget (OMB) Final Information Quality Bulletin for Peer Review (70 FR

2664-2677) (OMB Bulletin), and implementation of the Information Quality Act

(Pub. L. 106-554. ( https://www.usbr.gov/recman/cmp/cmp-p14.pdf )

b) The contractor will not have any formal involvement in the Peer Review process but will be required to be responsive to any outcomes of the peer review in the completion of the final report (Task 12).

https://www.usbr.gov/recman/cmp/cmp-p14.pdf

L. Task 12 - Report Finalization

a) The contractor, in collaboration with Reclamation, will address any outstanding questions and comments from Technical Team members received on the second draft Report on Tasks 2 through 8. Reclamation will make the final decisions on the content of the report.

b) Contractor will finalize the report to meet all Reclamation formatting standards.

M. Period of Performance

I. Period Start Date Completion Date

I. Contract duration Award Date Award Date plus 18 months (72 weeks)

Item

No.

Description Content Format Medium

Delivery:

Post Award

Date

1.

Monthly Progress

Rpt/Invoice Tasks 2-8 MS Word/pdf Digital

COR,

Monthly

2.

Project and Deliveries

Schedule Tasks 2-8

Tasks, Milestones

MS Project or similar

4 Weeks Post

Award (PA)

3. Review documents Task 1 NA Online

Resources 4 Weeks PA

4.

Draft Chapter: Flow

Analysis and Rpt Task 2

Reclamation

VI standards

MS Word/

Adobe pdf 12 Weeks PA

5.

Draft Chapter:

Water Temperature Task 3

Reclamation

VI standards

MS Word/

Adobe pdf 14 Weeks PA

6.

Draft Chapter:

Meteorology and

Lunar Data

Task 4 Reclamation

VI standards

MS Word/

Adobe pdf 16 Weeks PA

7.

Draft Chapter:

Water. Chemistry Task 5

Reclamation

VI standards

MS Word/

Adobe pdf 40 Weeks PA

8.

Draft Chapter:

Biological Task 6

Reclamation

VI standards

MS Word/

Adobe pdf 50 Weeks PA

9.

Draft Chapter:

Influences of K. R.

Dam Removal

Task 7 Reclamation

VI standards

MS Word/

Adobe pdf 52 Weeks PA

10.

Draft Chapter:

Flow Mgmnt Criteria Task 8

Reclamation

VI standards

MS Word/

Adobe pdf 53 Weeks PA

11. Draft Report Review Task 9 Reclamation

VI standards

MS Word/

Adobe pdf 59 Weeks PA

12.

Workshop:

Conceptual Model and

Recommendations

Task 10 Reclamation

VI standards

MS Word/

Adobe pdf 65 Weeks PA

13. Peer Review

(By Reclamation)

Task 11 Reclamation

VI standards

MS Word/

Adobe pdf 70 Weeks PA

14. Report Finalization Task 12 Reclamation

VI standards

MS Word/

Adobe pdf 72 Weeks PA

N. References

Asarian, J. E., K. De Juilio, S. Naman, D. Gaeuman, and T. Buxton. 2023. Synthesizing 87 years of scientific inquiry into Trinity River water temperatures. Report for the Trinity

River Restoration Program (TRRP). Riverbend Sciences, Eureka, California.

Belchik, M, D. Hillemeier, R. Pierce. The Klamath River Fish Kill of 2002: Analysis of

Contributing Factors. Yurok Tribal Fisheries Program. 42 pp

Bureau of Reclamation, 2013. Secretarial Determination Overview Report.

https://klamathrenewal.org/wp-content/uploads/2020/05/A7-Full-SDOR-accessible-

022216.pdf

Bureau of Reclamation, 2016. Environmental Assessment. 2016 Lower Klamath River Late-

Summer Flow Augmentation from Lewiston Dam. 39 pp.

Bureau of Reclamation. 2017. Long Term Plan to protect adult salmon EIS/ROD.

Bureau of Reclamation. 2021. Environmental Assessment EA-21-19-NCAO, 2021 Trinity

River Summer Flow Augmentation from Lewiston Dam. 35 pp.

Bureau of Reclamation. 2024. Final notes from 8 online meetings (July 18 to September 30, 2024) on Flow Augmentation Releases for the Lower Klamath River. Shasta Office, Shasta Lake, CA.

CDFW, 2004. September 2002 Klamath River Fish-Kill: Final Analysis of Contributing Factors and Impacts. July 2004. Northern California – North Coast Region. 183 pp.

Klamath River Renewal Corporation, 2022. Final Environmental Impact Statement for

Hydropower License Surrender and Decommissioning. 823 pp.

https://klamathrenewal.org/wp-content/uploads/2020/05/A7-Full-SDOR-accessible-022216.pdf https://klamathrenewal.org/wp-content/uploads/2020/05/A7-Full-SDOR-accessible-022216.pdf https://klamathrenewal.org/wp-content/uploads/2022/08/22_0826-3006_P-14803-Final-

EIS-Lower-Klamath-Hydrpelectric-Project.pdf

Moffett, J.W., and S.H. Smith. 1950. Biological Investigations of the Fishery Resources of the

Trinity River, California. Special Scientific Report No. 12. U.S. Fish and Wildlife

Service. 71 pp.

NOAA and USFWS, 2013. Memorandum to Brian Person, Reclamation Northern California

Area Manager, Subject: 2013 Fall Flow Release Recommendations. 46 pp.

National Research Council, 2004, Endangered and threatened fishes in the Klamath River

Basin—Causes of decline and strategies for recovery: Washington, DC, The National

Academies Press, https://doi.org/10.17226/10838 .

Snyder, J.O. 1931. “Salmon of the Klamath River, California.” Fish Bulletin No. 34. California

Department of Fish and Game. ( http://digitallib.oit.edu/digital/collection/kwl/id/556/ )

U.S. Fish and Wildlife Service, 2002. Klamath River Fish Die-off, September 2002. Mortality

Report. Arcata Fish and Wildlife Office, Arcata, CA. 35pp.

U.S. Fish and Wildlife Service, 2003. Klamath River Fish Die-off, September 2002. Causative

Factors of Mortality Report. Arcata Fish and Wildlife Office, Arcata, CA. 128pp.

https://klamathrenewal.org/wp-content/uploads/2022/08/22_0826-3006_P-14803-Final-EIS-Lower-Klamath-Hydrpelectric-Project.pdf https://klamathrenewal.org/wp-content/uploads/2022/08/22_0826-3006_P-14803-Final-EIS-Lower-Klamath-Hydrpelectric-Project.pdf https://doi.org/10.17226/10838 http://digitallib.oit.edu/digital/collection/kwl/id/556/