Summary

The Sacramento-San Joaquin Delta (the Delta) is formed by the confluence of two of California’s largest rivers: the Sacramento, flowing south from its headwaters near Mount Shasta, and the San Joaquin, flowing north from its origins in the southern Sierra Nevada mountains. These rivers and their tributaries carry about half of the state’s total annual runoff. Freshwater from the rivers mixes with saltwater from the San Francisco Bay and Pacific Ocean, forming one of the largest estuaries on the west coast of North America. The Delta, which spans about 738,000 acres in Northern California at the western edge of the Central Valley, is home to more than 627,000 people as well as 750 animal and plant species and 55 fish species.

Precipitation in California generally occurs between October and April, while municipal and industrial water demands are year-round, with agricultural demand at its highest during the growing season from April through August. To support growing demands for water supply development in California in the 20th century, two massive and interconnected systems of reservoirs, dams, and levees were constructed on the Sacramento and San Joaquin rivers: the Central Valley Project (CVP), overseen by the U.S. Bureau of Reclamation (USBR), and the State Water Project (SWP), overseen by the California Department of Water Resources (CDWR). The CVP can capture and store nearly 12 million acre-feet of water, and it delivers, on average, 7 million acre-feet of water a year from Northern California and the Sierra Nevada to support about 3 million acres of farmland, about 2 million people in urban centers, and 19 wildlife refuges, most of them in the Central Valley. The SWP can capture and store about 4.2 million acre-feet of water, and it delivers water, to 750,000 acres of farmland, mostly in the southern San Joaquin Valley, and to households (including 27 million Californians) and businesses throughout much of the state.

The CVP and SWP (referred to collectively as “the Projects”) rarely deliver their full contracted amount of water. Some of this is inherent in the operation of large water projects with diverse demands in a dry and highly variable climate. A growing, complex regulatory environment of state and federal laws, some of which were created to protect fish species endemic to the Delta, has further restricted CVP and SWP operations.¹ These fish include the southern distinct population segment of North American green sturgeon, California Central Valley steelhead, Central Valley spring-run Chinook salmon, Sacramento River winter-run Chinook salmon, longfin smelt, and Delta smelt. Operating the Projects while trying to prevent species extinction can be a source of conflict if the actions to prevent extinction reduce the amount of water that can be exported. Project operation into the future will likely become more challenging as changes in various climatic factors push the listed species closer to their thresholds

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¹ As discussed in Chapter 3, salinity and flow requirements control project exports to a greater extent than Endangered State Act requirements.

of survivability. Hence, in late 2023 USBR contracted with the National Academies of Sciences, Engineering, and Medicine to form an expert committee that could serve as an independent review for the CVP and SWP as they operate into the future. The Committee’s statement of task appears in Box S-1. The three actions chosen for the study—the Shasta Coldwater Pool Management Action, the Old and Middle River (OMR) Flow Management Action, and the Summer-Fall Habitat Action (SFHA) for Delta smelt—are perceived as consequential for species survival and controversial for their effects on water deliveries to contractors.

Chapters 2 through 4 discuss the three specific actions, providing a description of the action; evaluating the monitoring, modeling, and decision support tools relevant to the action; and identifying science challenges including how certain climate impact drivers will affect the action. Chapter 5 explores the organization of the science enterprise in the Delta region, overarching modeling issues, and the action agencies’ plans to address the increasing variability in precipitation and intensity of droughts as the actions are implemented into the future. Each chapter ends with conclusions and recommendations, the most important of which are compiled in this summary. Five appendixes provide relevant background information on California climate and hydrology (A), the history of California water resources development and major features of the Projects (B), the regulatory framework under which the CVP and SWP operate (C), the monitoring networks and modeling used in CVP and SWP operations (D), and a general overview of the seven fish species endemic to the Delta region that are listed as threatened or endangered under the Endangered Species Act (E).

SHASTA COLDWATER POOL MANAGEMENT

Shasta Reservoir, the largest storage reservoir in the CVP, is managed so that water is released to maintain flood conservation space, meet downstream flow and water delivery requirements, generate hydropower, and provide cold water to support populations of migrating winter-run Chinook salmon. Winter-run Chinook salmon histori-

cally migrated through the Delta and up the Sacramento River to spawn in the stable, cold, spring-fed headwaters of the Sacramento, Pit, and McCloud rivers during the summer. These historic spawning habitats were blocked by the construction of Shasta Reservoir, such that nearly all adult holding and spawning, as well as egg incubation and rearing, now takes place in an approximately 20 kilometer (km) reach of the Sacramento River below Keswick Dam, where summer water temperatures are much warmer. The Shasta Coldwater Pool Management Action aims to ensure that water cold enough to support winter-run Chinook adult holding and spawning and egg incubation is present in the reaches downstream of Keswick Dam over the summer months. To achieve this aim, USBR retains cold water in Shasta Reservoir until the summer and then operates a Temperature Control Device to blend water from warmer and colder layers within Shasta Reservoir during the appropriate summer months. The action is supported by a wide range of planning, monitoring, and modeling activities that assess physical and ecological conditions within the reservoir/river system. Finally, the action depends on the winter-run Chinook salmon hatchery program to supplement natural recruitment, particularly in drought years.

As explained in Chapter 2, the existing scientific understanding supports a three-pronged approach to Shasta Reservoir management: (1) continuing to improve temperature management downstream of Keswick Dam, which currently is where the only significant population of spawning winter-run Chinook salmon can be found; (2) continuing hatcheries management; and (3) reintroducing winter-run Chinook salmon above Shasta Dam and in Battle Creek, which will be essential to the protection and eventual recovery of the species. Over the long term, the third approach should increase operational flexibility as well as create diverse ecological benefits supportive of multiple species and life-history stages. The following specific recommendations are made.

Recommendations 2-1 and 2-2: USBR should enhance the monitoring of (1) Shasta Reservoir and (2) rivers relevant to the coldwater pool management action.

Temperature sensors for rivers and lakes are inexpensive to install and maintain. Additional sensors in key locations could provide information that enhances the predictive accuracy of the Water Temperature Modeling Platform, which USBR created to modernize the analytical tools that it uses to support activities and decision making for water temperature management in CVP reservoirs for fishery species protection in downstream river reaches. The installation of four to six Lake Diagnostic Systems throughout Shasta Reservoir would help operators better understand how high-frequency physical dynamics within the reservoir (such as seiching and internal waves) affect the thermocline depth and generate more accurate estimates of the coldwater pool volume.

Recommendation 2-3: High levels of “unattributed mortality” of winter-run Chinook salmon eggs must be better understood, through research that defines specific pathways for reducing said mortality, in order to develop management actions that can increase confidence in the use of egg-to-fry survival as the principal focus for coldwater pool management.

The focus on temperature-dependent mortality, interactive effects of multiple stressors, and fine-tuning of releases from the Shasta coldwater pool may increase survival, but even in years when temperature-dependent mortality is minimal, high mortality can still occur. Additional management actions supportive of winter-run survival can only be identified through an understanding of the influence of factors such as temperature, flow, habitat, substrate, pathogens, predation, and food quality and availability across all life stages. Ongoing studies investigating the temperature, dissolved oxygen levels, and flow through redds could evaluate the potential benefits of larger-scale actions such as channel and floodplain restoration, gravel augmentation, and pulse flows in sustaining pool-riffle sequences and other geomorphic features conducive to spawning.

Recommendation 2-4: As tribes, CDWR, and other groups continue feasibility studies, USBR should develop an actionable plan to facilitate and support the reintroduction of winter-run Chinook salmon to historic spawning and rearing habitat above Shasta Reservoir and in Battle Creek.

The challenges to and operational constraints on coldwater pool management presented by rising air temperatures, reduced snowpack, and increased drought intensity place winter-run Chinook salmon at increasing risk. The

only way to mitigate that risk, especially the risk of a catastrophic population crash associated with a more than three-year drought, is to safeguard some portion of the population in existing coldwater habitats.

OLD AND MIDDLE RIVER FLOW MANAGEMENT

The Projects divert large quantities of freshwater from the San Joaquin and Sacramento rivers, with some of the largest diversions occurring through the South Delta pumps: the C. W. “Bill” Jones Pumping Plant, operated by the San Luis & Delta-Mendota Water Authority for USBR, and the Harvey O. Banks Pumping Plant, operated by CDWR. Operation of the pumps can promote water flow away from the Sacramento and San Joaquin rivers and toward the South Delta, leading to entrainment of the listed fish species at both pumping facilities (“take”),² meaning they are drawn toward water intakes for the pumps along with flowing water. Other impacts to fish caused by the pumps include changes to Delta channel flow patterns that reroute fish to places where habitat conditions are less optimal for survival, prevent fish from completing their natural migration, and make fish increasingly subject to predation. Salvage of some entrained fish occurs at both pumping plants, and the salvaged fish are trucked to one of six locations near the confluence of the Sacramento and San Joaquin rivers.

The OMR Flow Management Action seeks to maximize the export of water while minimizing the adverse effects of pumping to fish populations when fish are rearing in and migrating through the Delta (December through June). The strategy is to limit exports during the migration season to control the magnitude of reverse flows in the OMR corridor just north of the pumps, based on real-time evaluation of environmental surrogates for Delta and longfin smelt and detections in salvage for winter-run and spring-run Chinook salmon and steelhead.

Chapter 3 makes three primary points. The OMR Flow Management Action, which uses fish “take” at the pumps, flow levels, and turbidity levels as triggers for placing limitations on pumping, has a reasonable scientific basis, although there are substantial uncertainties about how well each trigger correlates with fish protection. Reducing those uncertainties would require changes to monitoring and modeling. The most profound change would involve the development of a Delta-wide hydrodynamic model that enables mapping of the spatial and temporal influence of pumps, which in turn would allow water managers to move beyond management strategies that focus primarily on take at the pumps. The following specific recommendations are made.

Recommendation 3-1: The underlying scientific bases of the thresholds and corresponding export reductions used in OMR flow management should be made available so that their use can be appropriately reviewed.

Although it did not thoroughly analyze each threshold value, the Committee noted examples of thresholds that are not scientifically defendable. More thorough use of validated hydrodynamic models and particle tracking models could help defend or refine these values.

Recommendation 3-3: To move OMR flow management beyond the use of salvage as a proxy for impacts on fish in the Delta, the monitoring and modeling in support of the action should evolve to address the following four questions:

1. What is the zone (or sphere) of influence of operations? (2) What proportion of any given fish population is under that influence? (3) What is the impact to fishes in these regions? (4) What are the consequences of these impacts at the full population level? Several recommendations stem from adherence to this strategy.
   1. Fish spatial distribution and abundance throughout the Delta should be better assessed, using the latest technologies (e.g., underwater acoustics using both fixed and moving sensors, nocturnal aimed/instrumented midwater trawling) at higher temporal and spatial resolution than currently done.
   2. Expanded modeling efforts should build upon USBR’s zone of influence analysis to study changes in key factors such as temperature, submersed aquatic vegetation, salinity, and other water quality conditions

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² See Appendix C for a more complete legal definition of “take.”

across regions under a variety of Delta flow conditions, spanning dry to wet years, and under a range of pumping rates, using dimensionless flow ratios.

3. Ultimately, higher resolution, expanded domain, and multi-parameter integrated modeling is required for full assessment of the Delta-wide impacts of exports on hydrodynamics, water quality, and fish.

Recommendation 3-4: Improvements in Delta channels, forebays, infrastructure, and operations might help to reduce Delta-wide native fish losses and should be studied for their potential to reduce the ecological impacts of pumping.

Hydrodynamic models could help USBR and CDWR explore opportunities to both dampen tidal dispersion and reduce the pumps’ zone of influence via more effective Delta channels, forebays, fish screens, and tidal gates. USBR could assess the effects of building a separate forebay for the CVP, CDWR could assess ways to improve SWP forebay management, or the agencies could explore a joint forebay such as a flooded island.

SUMMER-FALL HABITAT ACTION FOR DELTA SMELT

Although the Delta smelt was once considered one of the most abundant fishes in the Delta, they are now extremely rare, with zero caught in most catch indices in recent years. The SFHA seeks to address a seasonal bottleneck for juvenile Delta smelt survival by providing more low-salinity habitat in the Suisun Marsh area during the summer and fall. The underlying hypothesis is that improving Delta smelt habitat by optimizing salinity, turbidity, temperature, and prey conditions, and by creating connectivity to food supplies, will support Delta smelt recruitment and population growth.

In its current form, the SFHA consists of three primary components: (1) management of the location of X2 (the 2 parts per thousand bottom salinity isohaline) in the fall and thereby the areal extent of the low-salinity conditions that favor Delta smelt, (2) operation of the Suisun Marsh Salinity Control Gates to adjust salinity in Suisun Marsh (and secondarily in Grizzly Bay) and possibly enhance food provision in the summer, and (3) an additional supplemental release of 100,000 acre-feet of freshwater.

Chapter 4 concludes that the greatest uncertainty about the SFHA is the inability to detect a response to the action in fish populations. Several targeted lines of research could accelerate better implementation of the SFHA and increase understanding of the effectiveness of various SFHA components, including genetic analyses (e.g., eDNA, DNA of predator guts), laboratory and field studies to analyze the species of zooplankton consumed by smelt, and mark-recapture technology for improved smelt detection. As with the other two actions reviewed by the Committee, it is unlikely that the SFHA will be sufficient to lead to Delta smelt persistence and recovery. Many more components of the SFHA, and other actions systemwide, will be needed to prevent extinction of this endemic Delta fish. The following specific conclusion and recommendations are made.

Conclusion 4-1: USBR and CDWR are to be commended for embracing an ecosystem-based approach to protecting Delta smelt that attempts to overlay Delta smelt distribution with food supplies and the favorable habitat conditions of the low-salinity zone.

However, over time some components of the SFHA believed to be necessary to generate food for resident native Delta fishes have been stopped. The action agencies are encouraged to pursue the identified special studies related to food and to commit to implementing the Suisun Marsh Salinity Control Gate component of the SFHA over multiple years in sequence.

Recommendation 4-1: Development of a process-based Delta smelt model in a spatial food-web context could greatly accelerate better implementation of the SFHA and increase understanding of the effectiveness of various SFHA components.

Ideally, this process-based model for Delta smelt and its prey would be linked to existing models on estuarine hydrodynamics and water quality, which would enable evaluation of how the SFHA ultimately affects Delta smelt

reproduction, growth, mortality, and seasonal movement. To achieve this level of prediction and analysis, monitoring may need to include the measurement of rates (e.g., zooplankton production) and not just static variables (e.g., standing crop) and should also examine zooplankton responses to action-mediated changes in water residence time. The Committee acknowledges that acquiring this modeling capacity will require targeted data collection and experimentation and possibly multi-year development horizons and investment across agencies.

Recommendation 4-3: An annual decision process for the SFHA founded on a series of environmental triggers that encompass more than water-year type should be considered.

Lessons from previous SFHA implementation, such as the 2017 Fall X2 action, show that the response of Delta smelt may be determined by environmental conditions that are unrelated to water-year type, including water temperature and antecedent conditions. The success of Fall X2 in a wet or above normal year may be dependent on the conditions in the previous year. A set of triggers (e.g., related to temperature and food resources) for the Suisun Marsh Salinity Control Gate could be established based on expectations developed early in the year, identifying under what conditions the action would proceed and how. Closer to the time of the action, monitoring data based on the triggers could be used to adjust SFHA implementation.

OVERARCHING ISSUES

Cross-cutting issues that emerged from the Committee’s analyses of Shasta coldwater pool management, OMR flow management, and the SFHA include the need to (1) enhance collaborative science to improve the pace and effectiveness of Bay-Delta watershed science efforts; (2) improve the modeling enterprise, with a focus on CalSim and ecological model integration; and (3) more strongly consider how changes in climate impact drivers will affect long-term operations. The following specific recommendations are made.

Recommendation 5-1: A formal feasibility study should be undertaken to assess the potential for a science hub for the Bay-Delta and its watershed.

This hub must be fit-for-purpose and grounded in the needs and culture of the science community. It should be designed to develop solutions to problems that are difficult to address within existing agency or academic silos, without interfering with agency mandates or diminishing internal capacity. It should enhance institutional expertise by creating a collaborative environment where new approaches can be developed and tested, monitoring can be better coordinated, and cross-agency training can be implemented. It would also facilitate better coordination across the science that supports CVP and SWP activities.

Recommendation 5-2: Finer-scale models are needed for water and ecosystem management in the Delta and its watershed.

In particular CalSim (which is now widely used to evaluate ecosystem impacts) would benefit from a finer time step (perhaps one week) coupled with explicit or empirical disaggregation to still finer ecologically relevant time steps. With such capability, CalSim (or some other model) could then provide systematic hydrologic information for the more fully coupled hydrodynamic and population models needed for ecosystem management. Innovative ecosystem-wide approaches and quantitative life-cycle models could help to identify management actions that can contribute to species recovery. Monitoring should be tailored and managed to provide data at the spatial and temporal scales needed by the models.

Recommendation 5-3: CDWR and USBR should coordinate more closely and develop shared standards and protocols for modeling climate change impacts on the CVP and SWP.

Consistent protocols are essential for minimizing uncertainty in projected climate change impacts, particularly those arising from two sources: future greenhouse gas emission scenarios and model-related uncertainties (e.g., climate sensitivity). Moreover, CDWR and USBR should regularly update their modeling protocols to ensure alignment with current best practices in climate impact assessment. Finally, given the increasing evidence of more frequent compound events (i.e., multiple extreme events occurring simultaneously) and cascading events (i.e., extremes occurring in sequence), there is a pressing need for more detailed modeling studies to assess how such events may affect the Projects.

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The three actions reviewed in this report are important elements of a broader effort to protect listed fish species while maintaining water-project operations. Each action has limitations and would benefit from improvements in related monitoring, modeling, and scientific understanding. In the near term, and perhaps for the long term, maintaining and fine-tuning these actions will be necessary for achieving key CVP and SWP goals. Nonetheless, taken in isolation the individual actions will be insufficient to achieve species recovery; rather, ecosystem-wide thinking on the part of action agencies will be imperative.

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