C05__Attachment_2_Asarian_etal_(2023)_Temperature_Synthesis_87_years.pdf

Sciences Riverbend

Synthesizing 87 years of scientific inquiry into Trinity River water temperatures

J. Eli Asarian Riverbend Sciences

Kyle De Juilio and David Gaeuman Yurok Tribe Fisheries Program, Trinity River Division

Seth Naman NOAA Fisheries

Todd Buxton U.S. Bureau of Reclamation

August 16, 2023

Trinity River Water Temperature Synthesis Report i

Synthesizing 87 years of scientific inquiry into Trinity River water temperatures

J. Eli Asarian Riverbend Sciences

Eureka, CA

Kyle De Juilio and David Gaeuman Yurok Tribe Fisheries Program, Trinity River Division

Willow Creek, CA

Seth Naman NOAA Fisheries

Arcata, CA

Todd Buxton U.S. Bureau of Reclamation

Weaverville, CA

Prepared for:

Trinity River Restoration Program

Weaverville, CA

August 16, 2023

Suggested citation:

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. 180 p. + appendices. Prepared for the Trinity River Restoration Program, Weaverville, California.

Photo credits for cover page:

Clockwise from top-left: Trinity River downstream of Eagle Creek (E. Asarian, 8/13/2017), temperature logger (E. Asarian), Trinity River at Bucktail channel rehabilitation site (Aaron Martin, 4/24/2019), Trinity Dam and Trinity Reservoir (U.S. Bureau of Reclamation, date unknown).

Trinity River Water Temperature Synthesis Report ii

EXECUTIVE SUMMARY

The Trinity River Record of Decision (ROD) was signed in 2000 to provide water and resources to aid restoration of fish and wildlife populations that were negatively affect by construction and operation of the Trinity River Division (TRD) of the Central Valley Project (CVP). The Trinity River Restoration Program (TRRP) provides an administrative and scientific framework to aid restoration of the Trinity River. The scientific framework included objectives that could be monitored, evaluated, and used to gage success in restoring anadromous fish populations and the ecological integrity of the river, notably with flow releases allocated according to water year types based on annual water yields (Critically Dry, Dry, Normal, Wet, and Extremely Wet).

In 2018, the Trinity Management Council (TMC), which oversees the TRRP, directed the TRRP to synthesize data, information, and learning that has occurred since the ROD. Accordingly, TRRP developed “synthesis reports” on fourteen topics to guide adaptive management. Because water releases from Lewiston Dam and their resulting temperatures at downstream locations are the primary drivers of biological populations in the Trinity River, the TRRP chose to develop a synthesis report focused on water temperatures. In this report, we compiled, summarized, analyzed, and modeled water temperature and hydrology data collected from the Trinity River, California to meet six objectives:

o Construct and populate a comprehensive quality-controlled water temperature dataset for analysis and archive it for future use;

o Evaluate patterns in the relationship between flow and temperature in space and time before the construction of the TRD, pre-ROD, and post-ROD;

o Evaluate how ROD flows have affected the thermal regime, temperature compliance, and biological objectives on the Trinity River;

o Evaluate temperature compliance across multiple years (pre-ROD and post-ROD);

o Update conceptual models on stream temperature dynamics in the Trinity River; and o Develop management recommendations to provide water temperatures in the Trinity

River that more efficiently meet restoration objectives of the TRRP.

We acquired river and tributary water temperature data from tribal, federal, state, and local agencies, consulting firms, and universities. The result is a set of stream temperature data for 252 sites at their original temporal resolution (sub-hourly to daily) compiled into a geographically referenced database containing 396,172 daily values, derived from 13 million original measurements. We also compiled hydrology and reservoir water temperature data in this database. These data were used to analyze existing conditions and develop model scenarios for pre-dam conditions and hypothetical management alternatives. From this effort, conceptual models were updated and used to explore water temperature dynamics on the Trinity River with comparisons made to regulated and unregulated rivers described in the literature.

Prior to construction of the TRD, the Trinity River exhibited complex temperature patterns that are normal to streams in regions with Mediterranean climates. These complex patterns span temporal, longitudinal, lateral, and vertical gradients, which drive the distribution, reproduction, growth, and migration of cold-blooded aquatic species such as fish, invertebrates, reptiles, and amphibians. Trinity and Lewiston dams and impacts from historic land use practices profoundly altered the thermal landscape in these dimensions, and regulated flow releases further

Trinity River Water Temperature Synthesis Report iii exacerbated temperature impacts on the Trinity River. For comparative analysis, we defined four eras associated with management changes: pre-dam era (10/1/1911–1/20/1961), full diversion era (10/31/1963–4/30/1978), transitional era (5/1/1978–9/30/1999), and ROD era (10/1/1999– 2019). ROD flows did not officially begin until Spring 2004, but we start the ROD era with hydrologic year 2000 because pre-ROD flows became increasingly similar to ROD flows.

When comparing the pre-dam era to the other eras, the largest impact to water temperatures in the Trinity River occurred at Lewiston. As is typical for rivers below large thermally-stratified reservoirs where water is released from cold depths, seasonal temperature variation has been severely reduced. With-dam seasonal minima and maxima have similar timing (January and August, respectively) as occurred pre-dam, but seasonal range in daily average temperatures has been compressed from 4–23 °C pre-dam to 7–10 °C with-dam. The flow regulation causes the river to be unnaturally warm in winter and cold in summer. Variation among years also declined at Lewiston from thermal dampening by the reservoir water bodies and the relative similarity of flow releases across years, regardless of annual variations in annual water yields or patterns in runoff. The downstream extent and severity of thermal impacts from the reservoirs and flow regulation varies with flows released from the dams. When dam releases are low, the thermal effects diminish more quickly than during high-flow releases when the entire length of the river below Lewiston Dam is strongly affected.

While the full diversion, transitional, and ROD era temperatures have more in common with one another than the pre-dam era, there are discernable management impacts associated with each era. Summer baseflows are a defining characteristic of each era and generally increased in magnitude to present. Spring and summer exhibited the greatest temperature change between eras, with increasing departure from unimpaired (i.e., pre-dam and pre-diversion) conditions as a result of less annual variation in flows, higher summer flows that extended cooler temperatures further downstream, and a shortened duration of warmer water temperatures in summer. Winter baseflows increased from 150 to 300 cfs in 1978 but are still much lower than the pre-dam era.

ROD flows were designed, in part, to meet temperature objectives for promoting salmonid populations. Temperature objectives for the Trinity River at Douglas City (18 miles downstream of Lewiston) and the North Fork Trinity River (40 miles downstream of Lewiston) were designed to protect salmonid adults, eggs, and embryos. Objectives at Weitchpec (located at the confluence with the Klamath River 112 miles downstream of Lewiston) were designed to provide suitable temperatures for smoltification (i.e., for juvenile salmonids to prepare for transition to saltwater), with any temperatures colder than the objectives considered sufficient or beneficial. Avoiding potentially detrimental effects of overly cold water were not prioritized during development of these criteria. Flow releases aimed at meeting these criteria have resulted in water that is so cold it can stunt the growth of juvenile salmonids and reduce their size at entry and survival in the ocean. With this in mind, we evaluated a new proposed temperature objective for optimizing juvenile salmonid growth at the confluence with the North Fork Trinity River.

During the ROD era, water temperatures at this site did not reach the optimal range for juvenile salmonid growth (13–16.5 °C) until a month later than in the transitional era and the modeled unimpaired flow scenario (i.e., pre-dam and pre-diversion). ROD-era temperatures were in the optimal range for only 18% of the primary rearing period (April–June), compared to 26% and 21%, respectively, for the transitional era and the modeled unimpaired flow scenario. Upstream at Douglas City, these patterns and differences were even more pronounced with optimal rearing temperatures in 10% of ROD era days, 29% of transitional era days, and 19% of days in the modeled unimpaired flow scenario. The timing and percent of days with optimal rearing

Trinity River Water Temperature Synthesis Report iv temperatures were relatively similar between the eras at Weitchpec because effects of the reservoirs and flow regulation on river water temperatures diminishes with downstream distance.

We evaluated compliance with temperature objectives in the ROD for the available period of record, which primarily spans the transitional and ROD eras, except at the Trinity River at Weitchpec where records also include the full diversion era. At Weitchpec, violations in temperature compliance were comparable between the transitional and ROD eras likely due to the similarity of managed flows, particularly baseflows, in these periods. While single temperature and location-based water temperature targets such as those at Weitchpec are simple to establish and evaluate, they inadequately assess whether the temporal and multi-dimensional temperature requirements in lotic systems are being met. We therefore recommend the development and implementation of a holistic approach to temperature management that assesses temperature objectives throughout the Trinity River.

Given the current inability to specify water temperatures released to the Trinity River, we investigated how adjusting flow releases from Lewiston Dam can better provide water temperatures that promote instream biology. The investigation compared ROD-specified flows to constant flows ranging from 300 to 4000 cfs and an unimpaired flow scenario. Results indicated that flows can be released from Lewiston Dam under current infrastructure constraints that would have substantially better biological effects than the current ROD flows. For example, the ROD specifies static winter baseflows (300 cfs) from October 15 through April 15, but our analyses indicated that increased flows in February and March in all water year types and in April of normal and wetter water years would provide temperatures that accelerate salmonid growth. Later, ROD flows that are elevated in comparison to unimpaired flows in late April through early summer supply cold water that suppresses salmonid growth, frog development, and benthic macroinvertebrates. The potential for lowering ROD flows in this period provides a significant opportunity for increasing the size and health of these populations in the Trinity River. Reducing flows to summer baseflow earlier in the year than under the ROD, particularly in normal, wet, and extremely wet years, would also benefit salmonid growth by allowing river temperatures to warm in a pattern that more closely mimics pre-dam water temperatures. Even if possible, we do not recommend returning temperatures entirely to the unimpaired scenario because access to high elevation, cold water habitat upstream of the dams has been lost.

However, there are important ecological services for species growth, development, and life history cues for reproduction and migration provided by the pre-dam temperature regime that should be emulated including appropriately timed spring warming and fall cooling.

Hydraulic mining and flow regulation have simplified some reaches of the Trinity River to a single-thread channel that lacks shallow edge habitats, side channels, and floodplain ponds.

Water temperatures are nearly uniform in these simplified reaches. We used modeling to show that channel rehabilitation work with heavy equipment that constructs shallow, slow-water habitats on the channel margins provides water temperatures that are warmer compared to deeper areas in the channel. The shallow, warm water substantially increases the range of water temperatures available to fish, invertebrates, amphibians, and reptiles. Our model results further indicated the temperature variations occurred during a wide range of seasons and flows, providing thermal habitat diversity capable of meeting the needs of a diverse aquatic species assemblage (e.g., Foothill Yellow-legged frog and salmonids).

We summarized potential impacts of climate change on Trinity River water temperatures using projected effects published in the scientific literature. Snowpack will decline substantially and

Trinity River Water Temperature Synthesis Report v winter rainfall will increase in the Trinity River basin as climate change increases air temperatures. The combination of more rain, less snow, and earlier snowmelt will cause earlier runoff and lower flows in spring and summer. Rising air temperatures will increase stream temperatures in all seasons, but warming will be greatest in spring and summer due to the aforementioned changes in hydrology. Reducing global greenhouse gas emissions would reduce the severity of these effects. In line with climate change projections, our analysis of long-term data showed that Trinity Reservoir temperatures have warmed in recent decades, even in the deepest and coldest portions of the reservoir. Trinity Reservoir is expected to be substantially impacted by climate change with warmer release temperatures caused by warmer inflow temperatures and lower end of September storage volumes that will result from increased water demand, earlier runoff, and the need to maintain greater flood control capacity.

Management of water temperatures released to the Trinity River are provided by the main and auxiliary outlet works of Trinity Dam, flow management through Lewiston Reservoir, and Trinity Reservoir storage. Both low Trinity Reservoir storage and low flows through Lewiston Reservoir can result in warm water releases to the river, which is most common in fall when salmon are spawning. While temperatures for juvenile salmonid rearing is a concern in spring, providing cold water temperatures for adult salmonids and their eggs becomes vital in late summer and fall. When the reservoir is drawn down to low levels (<0.75 million acre-feet), temperatures in the main outlet of Trinity Reservoir can exceed the thermal tolerance of salmonid eggs, the life stage that is most temperature sensitive. This can pose a risk to populations and require cold water releases from the auxiliary outlet works that bypasses turbines that generate electricity, such as occurred during severe droughts in 1977, 2014, and 2015. Had these droughts persisted for another year, even the auxiliary outlet may not have been cold enough to protect incubating eggs. With climate change, greater emphasis will need to be placed on conserving the cold-water pool in Trinity Reservoir, much like is currently adopted in Shasta Reservoir management.

Summary of important findings or confirmation of prior findings:

• Water released from Lewiston Dam into the Trinity River is nearly always too cold to support optimal juvenile salmonid growth during the primary rearing period (April-June).

• Elevating Lewiston Dam releases above 300 cfs winter baseflows before April in Dry years and May in Normal and wetter years would provide temperatures that benefit salmonids, invertebrates, and frogs by increasing food assimilation and development rates.

• April in Dry years and May in Normal and wetter years are the only time periods in spring when it is possible for temperatures in the entire Lewiston to Weitchpec reach of the Trinity River to approximate unimpaired (i.e., pre-dam) patterns.

• In May of Dry years and June of Normal and wetter years, elevated releases suppress growth of cold-blooded aquatic species.

• To provide cool water for meeting outmigration temperature criteria at Weitchpec, the ROD required large spring releases but did not consider the deleterious effects of these releases on juvenile salmonid growth in upstream reaches.

• Trinity Reservoir storage <0.75 million acre-feet in September, October, and November poses a notable risk of water releases that exceed the thermal tolerance of salmonid eggs and can cause mortality.

Trinity River Water Temperature Synthesis Report vi

• Trinity Reservoir storage is likely to decrease and water temperatures are likely to increase in the future due to changes in runoff patterns from climate change.

• It is not clear that ROD water management has resulted in increased temperature compliance from the period of record available.

Based on our assessments, we make the following recommendations:

1. Monitor temperatures in the Trinity River upstream of Trinity Reservoir to better understand the natural temperature regime and its effects on water temperatures in Trinity Reservoir.

2. Flows in spring should recede beginning in April of Dry and Critically Dry water years and May of Normal and wetter water years to provide water temperatures in the Trinity River upstream of the North Fork Trinity River within the range that provides optimal juvenile salmonid growth (13–16.5 °C) and outmigration (16–18 °C).

3. Reduced emphasis on meeting ROD temperature targets for smoltification at Weitchpec.

Instead, the goal should be a balance between growth, encouraging timely outmigration, and mitigating temperatures in the lower river that approach the thermal limits of juvenile salmonids.

4. Infrastructure of the TRD should be modified to enable finer flow and temperature management to be implemented for the benefit of the river ecosystem, including:

a. Installation of a multi-level temperature control device in Trinity Reservoir;

b. Removal of Lewiston Dam or construction of a new type of conveyance through or around Lewiston.

5. For Trinity Reservoir, an end of September storage minimum of 0.75 million acre-feet

(MAF) should be adhered to following the recommendations of Bender (2012). This should be coupled with a multi-year drought contingency plan that specifies steps taken when reservoir storage is predicted to be less than 1.25 MAF in any year, assuming a multi-year drought is possible at any time.

6. An assessment of multiyear drought effects on Trinity Reservoir storage levels, water temperatures, and the resulting ability to meet temperature criteria in the Trinity River should be conducted.

7. Development of a tool for accurately predicting Trinity River water temperatures in summer at flows lower than RBM10’s current lower limit of around 350 cfs.

Trinity River Water Temperature Synthesis Report vii

Figure ES-1. Conceptual model of the Trinity River and its reservoirs, showing key drivers of thermal dynamics and highlighting important management issues and biological effects.

Trinity Reservoir

Mountain snowpack controls spring runoff in Trinity Alps tributaries including upstream of reservoir

Trinity Dam Releases deep cold water, including deeper/colder auxiliary outlet when necessary Expensive retrofit to multilevel outlets could allow warmer water releases in spring

Lewiston Reservoir:

Amount of warming depends on residence time, decreased since 1990s due to higher river flow and more warm-season diversions

Unregulated tributaries including upstream of dam

Thermal regime of largest tributaries similar to pre-dam river

Trinity Reservoir Regulates flow Thermally stratified in Mar–Dec (warm at surface, cold at depth) Cold pool depleted during severe droughts

Carr Diversion transfers ~50% of annual reservoir inflow to

Central Valley farms

Most tributaries to Upper Trinity R. are warmer than river in late spring and summer

Cooling effect of Trinity R.

on Klamath R. depends on dam releases, time of year, and weather (greater cooling when hot)

Small tributaries to Lower Trinity R. are cooler than river, providing summer/fall thermal refugia

Klamath River is warmer than Trinity R. when unnaturally high volumes of cold water are released from Trinity Reservoir, otherwise similar temperatures

Lewiston Dam

Lower Trinity R.

Effects of dam releases vary with season, tributary temperatures, and ratio of dam releases to tributary flow ROD-specified high flow releases in late May to early July are intended to maintain cool temperatures in Lower Trinity R. for smolts, even though this makes temperatures as much as 3 °C cooler than pre-dam 450 cfs summer baseflow releases have little cooling effect (<1 °C) because travel time is slow enough for water to warm up

Spring and early summer temperatures cool in high-flow years, warm in low-flow years Temperatures warm up as flow declines in spring, are hot in mid-summer

Lewiston to Douglas City

Release temperatures almost always cold, so dam release quantity has relatively little effect at dam if Carr Tunnel diversions are high enough to minimize warming through Lewiston Reservoir.

Drawdown of Trinity Reservoir elevates dam release temperatures

450 cfs summer baseflow is much higher than natural.

Provides cold water for adult spring chinook holding, replacing inaccessible habitat above dam where salmon held in thermally-stratified pools prior to dams

Douglas City to North Fork

Temperatures highly affected by dam release quantity

NF

Trinity

R.

Pulse flow dam releases in late summer and early fall for Hoopa Boat Dance and Lower Klamath fish health have large cooling effect With ROD spring high flow releases, temperatures are too cold (<13 °C) for optimal juvenile chinook salmon growth until after most juveniles have already migrated downstream…

…late May in dry and critically dry water years, and early July in other water year types

…mid-June in dry and critically dry water years, and early July in other water year types

Climate change causing less snow, more rain, and earlier runoff

Chanel rehabilitation seeks to replace thermally-diverse off-channel and edge habitats lost from geomorphic effects of dams and mining

Trinity River Water Temperature Synthesis Report viii

TABLE OF CONTENTS

Executive Summary .................................................................................................................................................................. ii Table of Contents ................................................................................................................................................................... viii List of Electronic appendices .................................................................................................................................................. xi List of Figures .......................................................................................................................................................................... xii List of Tables ......................................................................................................................................................................... xvii 1 Introduction

1.1 Purpose, need, scope, definitions, and objectives

1.2 Stream temperature basics

1.2.1 Physical drivers of thermal dynamics

1.2.2 Temperature effects on stream biota

1.3 Overview of the Trinity River Watershed

1.4 Trinity River Restoration

1.4.1 Temperature objectives

1.4.2 Flow management and hypotheses

1.4.2.1 Ascending Limb of snowmelt Peak Flow (April 22 to May 24)

1.4.2.2 Descending Limb of Snowmelt Peak (May 5 to July 22)

1.4.2.3 Summer/Fall Baseflow (June 26 to October 15)

2 Data and methods

2.1 Available data and reports

2.2 Available temperature models

2.3 Analytical methods

2.3.1 Statistical

2.3.2 Filling gaps in Lewiston water temperature record

2.3.2.1 Gaps due to gage relocation

2.3.2.2 Other gaps

2.3.3 Modeling

2.3.3.1 Improvements to RBM10 model boundary conditions

2.3.3.2 RBM10 scenarios

2.3.3.3 RBM10 issues to be resolved in future model updates

2.3.4 Defining thermal regimes eras

2.3.5 Units

3 Stream temperature dynamics of the Trinity River and tributaries

3.1 Conceptual model of reservoir / river thermal dynamics

3.2 Unregulated tributaries including upstream of Trinity Reservoir

3.3 Reservoir and dam operations

3.3.1 Trinity Dam

3.3.1.1 Physical characterization of dam, reservoir, and outlet works

3.3.1.2 Reservoir temperature dynamics, cold water storage pool, and dam release temperatures

3.3.2 Lewiston Dam, diversion, and fish hatchery

3.3.2.1 Physical characterization of dam, reservoir, diversions and outlet works, fish hatchery

3.3.2.2 Influence of dam operations and water diversions on temperature dynamics

3.3.2.3 Influence of hatchery operations on temperature dynamics

3.4 Trinity River flow and temperature regime below Lewiston Dam

3.4.1 Comparison of natural, unregulated flows to regulated flows with dam operations

3.4.1.1 Modeling unimpaired Lewiston flows

3.4.1.2 Modeling unregulated Lewiston temperatures

3.4.1.3 Summary of effects of dams on Lewiston flows and temperature

3.4.1.4 Dam and diversion effects on river temperatures from Lewiston to Weitchpec

3.4.2 Ambient effects

3.4.2.1 Air temperature and solar radiation

3.4.2.2 Shading

3.4.2.3 Wildfire smoke

3.4.3 Tributary effects on mainstem conditions

3.4.3.1 flow

3.4.3.2 Temperature

3.4.4 Effects of flow regulation on river temperatures

3.4.4.1 Thermally stable nodes and antinodes resulting from flow regulation

3.4.4.2 Diel temperature patterns

3.4.5 Temperature effects of 2000 Record of Decision (ROD) flow releases

Trinity River Water Temperature Synthesis Report ix

3.4.5.1 Compare pre-dam, pre-ROD, and post ROD temperature regimes

3.4.5.2 Effect of ROD water volume allocation (varies by water year)

3.4.5.3 Effect of hydrograph components on river temperatures

3.4.6 Temperature effects of other flow releases (Non-ROD)

3.4.6.1 Winter/spring Safety of Dams releases

3.4.6.3 Summer pulse flows for Hoopa Valley Tribal Boat Dance Ceremony

3.4.6.4 Summer/fall releases to increase flow in the Lower Klamath River

3.4.6.5 Emergency releases

4 Trinity River mainstem temperature criteria

4.1 Existing temperature criteria

4.1.1 Summary of numeric temperature criteria

4.1.2 What was considered in development of criteria

4.1.2.1 Adult criteria

4.1.2.2 Outmigration and smoltification criteria

4.1.2.3 Cold temperatures were generally not considered a problem

4.1.3 Scientific understanding has evolved since criteria were developed

4.1.3.1 Importance of Juvenile salmon growth criteria

4.1.3.2 Improvement in understanding dam/diversion effects on lower Trinity River temperatures

4.2 New proposed temperature targets

4.2.1 Target for juvenile salmonid growth

4.2.2 Target for adult spawning and egg incubation

4.3 Multi-year evaluation of temperature criteria exceedance

4.3.1 Exceedance of existing criteria for adults and juvenile outmigration

4.3.2 Exceedances of proposed juvenile growth target

5 Importance of thermal diversity

5.1 4-Dimensions of the lotic thermal landscape

5.1.1 Temporal thermal diversity

5.1.2 Longitudinal thermal diversity

5.1.2.1 Temperature modeling methods - longitudinal and seasonal dimensions

5.1.2.2 Temperature modeling results - longitudinal and seasonal dimensions

5.1.3 Vertical thermal diversity

5.1.4 Lateral thermal dimension

5.1.4.1 Hydraulic/temperature modeling methods - lateral dimension

5.1.4.2 Hydraulic/temperature modeling results - lateral dimension

5.2 Discussion of thermal diversity modeling results

5.2.1 Longitudinal and seasonal dimensions

5.2.2 Lateral dimension

5.3 Recommendations

5.3.1 Longitudinal and seasonal dimensions

5.3.2 Lateral dimension

6 Climate change

6.1 Projections for air temperature, precipitation, snowpack, streamflow, and reservoir storage

6.2 Projections for stream temperature

6.3 Long-term trends for reservoir and stream temperatures

7 Discussion

7.1 Current Trinity River water temperature regime

7.1.1 Ascending limb of snowmelt peak (April 22 – May 24)

7.1.2 Descending limb of snowmelt peak (May 5 to July 22)

7.1.3 Summer/fall baseflow (June 26 to October 15)

7.2 Trinity Reservoir

7.2.1 Storage

7.2.2 Infrastructure

7.3 Climate change

8 Recommendations 9 References Appendix A Details on available reports, models, and data ......................................................................................... A1

A.1 Summary of previous reports ...................................................................................................................................... A1 A.2 Additional information on temperature models .......................................................................................................... A1

A.2.1 Reservoir ........................................................................................................................................................... A1 A.2.2 River .................................................................................................................................................................. A2

Trinity River Water Temperature Synthesis Report x

A.3 Stream temperature data (continuous and/or daily) .................................................................................................... A3 A.3.1 Yurok Tribe Fisheries Program ......................................................................................................................... A3 A.3.2 Yurok Tribe Environmental Program ................................................................................................................ A7 A.3.3 U.S. Forest Service ............................................................................................................................................ A7 A.3.4 U.S Fish and Wildlife Service ........................................................................................................................... A8

A.3.4.1 Microsoft Access database of current data ................................................................................................................ A8 A.3.4.2 Klamath/Trinity data not in current version of USFWS database (1997–2005) ........................................................ A8 A.3.4.3 Trinity River at Lewiston from Moffett and Smith (1942–1946) .............................................................................. A8 A.3.4.4 Trinity River mainstem data from annual flow evaluation reports (1987–1989) ....................................................... A8 A.3.4.5 Trinity River mainstem and Tributary data from Zedonis (1988–1994) .................................................................... A9 A.3.4.6 Tributaries of the Lower Klamath River and Trinity River (1977–1978) .................................................................. A9 A.3.4.7 New River (1989–1998) .......................................................................................................................................... A10 A.3.4.8 Blue Creek (1988–1993) ......................................................................................................................................... A10 A.3.4.9 Lower Klamath River (1995) .................................................................................................................................. A10 A.3.4.10 Klamath River at Big Bar Trap (1991–2000) .......................................................................................................... A10 A.3.4.11 Trinity river and tributaries (1999) .......................................................................................................................... A10 A.3.4.12 Mainstem Klamath and Trinity River sonde data (2001–2005) ............................................................................... A11

A.3.5 U.S. Geological Survey ................................................................................................................................... A11 A.3.6 California Data Exchange Center (CDEC) ...................................................................................................... A11 A.3.7 California Department of Water Resources ..................................................................................................... A11 A.3.8 U.S. Bureau of Reclamation ............................................................................................................................ A11 A.3.9 Hoopa Valley Tribal Environmental Protection Agency (HVTEPA) ............................................................. A12 A.3.10 California Department of Fish And Wildlife .............................................................................................. A12 A.3.11 Murray Reports on Lewiston Fish Trapping Facilities (1958–1961) .......................................................... A13 A.3.12 Trinity County Planning Department and Watercourse Engineering ......................................................... A13 A.3.13 Five Counties Salmonid Conservation Program ......................................................................................... A14 A.3.14 Additional stream temperature datasets acquired but not compiled or not used in analysis ....................... A14

A.3.14.1 U.S. Forest Service, Redwood Sciences Lab ........................................................................................................... A14 A.3.14.2 Humboldt State University's Forest Science Project................................................................................................ A14 A.3.14.3 Riverbend Sciences ................................................................................................................................................. A14 A.3.14.4 The Watershed Research And Training Center ....................................................................................................... A15 A.3.14.5 Green Diamond Resource Company ....................................................................................................................... A15 A.3.14.6 Graham Matthews and Associates ........................................................................................................................... A15 A.3.14.7 Oregon State University .......................................................................................................................................... A15 A.3.14.8 Additional stream temperature datasets not acquired or compiled, or are no longer available ................................ A15

A.4 Trinity Reservoir temperatures ................................................................................................................................. A16 A.5 Other water temperature data .................................................................................................................................... A16

A.5.1 Lewiston Reservoir temperatures .................................................................................................................... A16 A.5.2 Thermal Infrared.............................................................................................................................................. A17 A.5.3 NorWeST stream temperature model .............................................................................................................. A17 A.5.4 Historical field measurements associated with water quality sample collection ............................................. A17

A.6 Hydrology data ......................................................................................................................................................... A18 A.7 Meteorological data .................................................................................................................................................. A18

Appendix B Analytical methods ..................................................................................................................................... B1 B.1 Linear regression ......................................................................................................................................................... B1 B.2 LOESS regression ....................................................................................................................................................... B1 B.3 Linear mixed-effects models ....................................................................................................................................... B1 B.4 Generalized additive [mixed] models (GAM and GAMM) ........................................................................................ B2 B.5 Supplemental method for modeling unimpaired Lewiston flows ............................................................................... B2 B.6 Filling gaps in Lewiston water temperature record ..................................................................................................... B4 B.7 Extending water temperature period of record and filling gaps at other Trinity River sites ....................................... B5 B.8 Extending water temperature period of record and filling gaps at tributary sites ....................................................... B5 B.9 Spatiotemporal interpolation of Trinity Reservoir temperature profiles ..................................................................... B7 B.10 Temperature modeling methods – longitudinal and seasonal dimensions .................................................................. B8 B.11 Hydraulic/temperature modeling methods -lateral dimension .................................................................................... B8

Appendix C Suplemental results and literature summaries ......................................................................................... C1 C.1 Trinity Reservoir thermal dynamics ........................................................................................................................... C1 C.2 Travel time .................................................................................................................................................................. C1

C.2.1 Limerinos (1967) dye release study .................................................................................................................. C2 C.2.2 Trinity River sub-daily model (Watercourse Engineering 2007) ...................................................................... C5 C.2.3 Comparison of gaged flows during changes in dam releases ............................................................................ C6

C.3 Longitudinal and seasonal temperature modeling of daily thermal effects Of dam release magnitude ...................... C7

Trinity River Water Temperature Synthesis Report xi

LIST OF ELECTRONIC APPENDICES

These will be available on the TRRP DataPort (https://www.trrp.net/library/)

ELECTRONIC APPENDIX 1: MS Excel spreadsheet of stream temperature data for 1942–2019, including: a) daily summary table, b) annual summary table, c) site location table, and d) pivot charts for data exploration.

ELECTRONIC APPENDIX 2: comma-delimited text file (.csv) versions of the same data tables that are in Electronic Appendix 1.

ELECTRONIC APPENDIX 3: The original temporal resolution (15–120 minute) stream temperature data for 1990–2019 were too large for Excel (limited to 1 million rows), so instead are provided as a separate comma-delimited text file (.csv).

ELECTRONIC APPENDIX 4: Gap-filled water temperatures for several mainstem Trinity River sites: at Lewiston (daily min, mean, and max 1981–2019), at Douglas City (daily mean only 1987–2019), upstream of North Fork (daily mean only 1987–2019), and at Weitchpec (daily mean only 1964–2019).

We did not gap-fill Lewiston 1942–1980, but include the measured data for the period as a convenience for future users.

ELECTRONIC APPENDIX 5: Daily mean temperature and flow estimates for Trinity River at Lewiston under no-dam scenario with unimpaired flow and unimpaired temperature, 1963–2019.

ELECTRONIC APPENDIX 6: Water temperature depth profiles for Trinity Reservoir measured by the U.S. Bureau of Reclamation approximately monthly, 1972–1990 and 1998–2020 (USBR 2020).

ELECTRONIC APPENDIX 7: U.S. Bureau of Reclamation hourly water releases from TRN – Trinity Lake, Trinity Dam, and Trinity Powerplant, January 2000 – February 2020.

Note: during the course of this project, we obtained many reports and datasets relevant to the Trinity River. We arranged to have many of these reports uploaded to the TRRP DataPort (https://www.trrp.net/library/) where future users can find them by searching on author name or title. In addition, the model input, output, and code files from the BETTER water temperature model for Lewiston Reservoir (JSA 1992, Kamman 1999b) have now been uploaded to the DataPort as a data package (Kamman 1999a).

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LIST OF FIGURES

Figure ES-1. Conceptual model of the Trinity River and its reservoirs, showing key drivers of thermal dynamics and highlighting important management issues and biological effects. ............................................................................. vii

Figure 2. Energy and hydrological exchanges determining stream temperature Figure 3. Mean daily and diel variability of water temperatures as a function of stream order/downstream direction for a typical river, not representative of the dam-regulated mainstem Trinity River (from Caissie 2006) Figure 4. Releases from Lewiston Dam into the Trinity River proposed in the ROD by water year Figure 5. Sources, sites, and dates of mainstem Trinity River water temperature data compiled for use in this project, 1942–

2020. us = upstream, rm = river mile Figure 6. Comparison of daily water temperatures at sites near Lewiston Dam for example years before and after the May 22, 2011 relocation of station LWS upstream to a new location (LWSnew) influenced by the hatchery outfall and not representative of true river temperatures (i.e., daily max temperatures much higher at LWSnew than TRBL1 in summers 2017–2018)

Figure 7. Water temperatures measured from 1990–2019 in major tributaries as well as the Trinity River upstream of Trinity Reservoir, with sites labeled and sorted by drainage area in square kilometers (km2)

Figure 8. Overview of Trinity Dam and associated structures Figure 9. Schematic of spillways and outlet facilities at Trinity Dam (Wahl and Cohen 1999) Figure 10. Water temperature depth profiles in Trinity Reservoir measured in the years 1973–2019 by USBR (2020), arranged clockwise by month Figure 11. Trinity Reservoir time series for 1972–2019: (A) air temperatures from PRISM (Daly et al. 2008), (B) Trinity River flows above Coffee Creek from USGS, (C) water temperature depth profiles measured approximately monthly by USBR (2020), (D) weekly estimates of water temperature at 2-ft depth intervals interpolated from the measured profiles using fixed rank kriging, (E) water temperature at the depths of the main (2114 ft) and auxiliary outlets (1999.5 ft)

Figure 12. Seasonal patterns of water temperatures in Trinity Reservoir at elevations of the 28 ft diameter main outlet (centerline of 2114 ft) and auxiliary outlet (2000 ft) in the years 1972–2019

Figure 13. Comparison of the 1972–1990 and 1998–2019 time periods for the relationship of Trinity Reservoir storage volume to water temperatures at elevations of main outlet (2114 ft) and auxiliary outlet (2000 ft) for all months (January– December) in 38 years from 1972–2019, excluding years without data

Figure 14. Relationship of Trinity Reservoir storage volume to water temperatures at main outlet elevation (2114 ft) for all months (January–December) in 38 years from 1972–2019, excluding years without data

Figure 15. Reservoir water storage in Trinity Reservoir from November 1960 to September 2019. Data from USGS site 11525400. Dashed line at 0.75 million acre-feet (MAF) indicates the carryover storage level below which may be potentially thermally problematic for cold water fish in the Trinity River (Bender 2012)

Figure 16. Lewiston Dam and associated points of diversion and other facilities. Figure from USBR (2012) Figure 17. Elevations of features relative to Lewiston Dam (USBR 2012) Figure 18. Comparison of monthly flow timing in the Trinity River at Lewiston (USGS gage 11525500) and the Carr Diversion

(USGS gage 11525430) for three eras: pre-dam (10/1/1911–1/20/1961), with-dam full diversion (10/31/1963– 4/30/1978), with-dam transitional (5/1/1978–9/30/1999), and with-dam ROD (10/1/1999–2019). The total outflow of Lewiston Reservoir is sum of these two sites

Figure 19. Time series of daily mean outflows from Lewiston Reservoir for hydrologic years 1963–2019 in the months of March–October

Figure 20. Lewiston Reservoir daily time series for 2000–2019: (A) Flow releases from Trinity Reservoir into Lewiston Reservoir, (B) water temperature at depths of main (2114 ft) and auxiliary outlets (1999.5 ft) in Trinity Reservoir from daily interpolation of USBR (2020) monthly measured profiles, and measured gap-filled temperatures at the Trinity River gage below Lewiston Dam from CDEC and USFWS

Trinity River Water Temperature Synthesis Report xiii

Figure 21. Comparison of daily measured flow in the Trinity River above Coffee Creek (USGS gage 11523200) and reservoir inflow calculated from water balance (3-day average of CDEC CLE). Horizontal dotted line at 28 cfs indicates the minimum 1911–1961 pre-dam flow measured in the Trinity River at Lewiston (USGS gage 11525500). Graph and regression were restricted to gaged flows less than 250 cfs

Figure 22. Comparison of measured and leave-one-year-out cross-validated predictions for daily mean water temperatures in the Trinity River at Lewiston for 1942–1946 and 1958–1961, prior to dam regulation. Model uses air temperature, flow, day of year, and autocorrelation. Data sources for observed water temperature: Moffett and Smith (1950), Murray (1960, 1961), and USGS (gage 11525500)

Figure 23. Daily time series of air temperature, water temperature, and flow for the Trinity River at Lewiston for 1942–1946 and 1958–1961, prior to dam regulation. Data sources: air temperature from gridded models (Livneh et al. 2013, Daly et al. 2008); measured water temperature from Moffett and Smith (1950), Murray (1960, 1961), and USGS (gage 11525500); modeled water temperature data from our analysis; and flow from USGS (gage 11525500)

Figure 24. Daily mean flow time series for the Trinity River at Lewiston for each year 1962–2019, comparing measured flows to a modeled unimpaired flow scenario without dams and diversion

Figure 25. Daily mean temperature time series for the Trinity River at Lewiston for each year 1962–2019, comparing measured temperatures to a modeled unimpaired flow scenario without dams and diversion. Ribbon around model prediction line is ± 0.94°C, the root mean squared error (RMSE) from model cross-validation (Figure 22)

Figure 26. Daily time series of water temperature and flow for the Trinity River at Lewiston for each year 1911–2019, comparing the pre-dam era (10/1/1911–1/20/1961), with-dam full diversion era (10/31/1963–4/30/1978), with-dam transitional era (5/1/1978–9/30/1999), and with-dam ROD era (10/1/1999–2019), and a modeled unimpaired flow scenario (1963–2019) without the dams and diversion

Figure 27. Daily mean water temperature time series for Trinity River at Lewiston 1963–2019, colored by water year type, showing (A) temperatures in a modeled no-dams unimpaired flow scenario, (B) measured with-dam temperatures, and (C) difference between the two

Figure 28. Modeled average monthly water temperatures at several locations of the Trinity River before and after construction of the Trinity River Division. Figure adapted from Frederiksen, Kamine and Associates (1980) and Zedonis and Newcomb (1997), but original source is Rowell (1979)

Figure 29. Daily mean water temperatures for the months of January–July at selected mainstem Trinity River sites modeled with RBM10 comparing two scenarios (no-dam unimpaired flow and constant 350 cfs dam release) and condensed actual water year types (Dry/Critically Dry and Normal/Wet/Extremely Wet) for years 1980–2018. The RBM10 model was not calibrated for Lewiston releases less than 350, so days with unimpaired Lewiston releases less than 350 cfs are not shown

Figure 30. Average monthly river flow (A) and water temperatures (B) at Lewiston before and after construction of the Trinity River Division in 1963

Figure 31. Profile of the Trinity River showing drainage area (km2 = square kilometers) and major tributaries from headwaters to its mouth where it flows into the Klamath River

Figure 32. Daily flow at selected mainstem Trinity River sites as a ratio of Lewiston releases, from the RBM10 historical scenario for each year 2000–2018. Flows from RBM10 model

Figure 33. Seasonal patterns in 2000–2018 daily flow at selected mainstem Trinity River sites as a ratio of Lewiston releases, comparing the RBM10 historical dam-regulated flow scenario and unimpaired (i.e., no dams or diversion) flow scenario. Flows from RBM10 model

Figure 34. Profile of RBM10-modeled monthly mean mainstem Trinity River temperatures by river mile, for the years 2000– 2018 under the historical scenario

Figure 35. Profile of RBM10-modeled monthly mean mainstem Trinity River temperatures by river mile, for the years 2000– 2018 under a scenario with Lewiston releases set to unimpaired flows and without-dam temperatures

Figure 36. Measured…