The release of hatchery-reared fish into the natural environment for conservation purposes may have unintended consequences for wild fish populations and the larger ecosystem. In situ enclosures are a tool that can be used to study cultured fish under natural conditions to help mitigate these risks or to acclimate fish to the surrounding environment during soft release. Despite widespread utility, few resources provide direction on material choice and enclosure design to conserve non-commercial and imperiled fish species that may have unique physiology and needs. Here, we designed, created, and tested an enclosure for the endangered Delta Smelt (Hypomesus transpacificus), an osmerid native to the San Francisco Estuary (estuary). We first performed hydraulic modeling and evaluated permeability to prey items by measuring energy dissipation and flow deflection of candidate screen materials in a flume. The final enclosure design was a cylinder made out of stainless-steel wire mesh, with 60% openness that measured 1.0 m in diameter and 1.3 m tall. We then investigated survival, growth, and feeding of cultured Delta Smelt in the enclosure in three 1-month-long deployments in an experimental pond. Fish survival was moderate to high (50% to 93%), and we observed that Delta Smelt in the enclosures spontaneously converted to live, natural food, which suggests that cultured fish will be able to forage when released into the estuary. We hope that the steps we have outlined and the final enclosure design will be instrumental in supplementing Delta Smelt and conserving other at-risk fish species in the future.
Current ecological conditions in the San Francisco Estuary are considered inhospitable to many native estuarine species, and have placed the endemic Delta Smelt (Hypomesus transpacificus) at serious risk. Programmatic monitoring regimes conducted by government agencies are insufficient for associating Delta Smelt occurrence with relevant habitat attributes, which limits inference about the relationships between putative habitat, restoration activities, and population response. Indirect observation of macro-organisms via detection of environmental DNA (eDNA) has proved a compelling alternative monitoring approach, particularly for rare and/or protected species. Yet, factors that influence eDNA detection in estuarine habitats remain poorly characterized, which hinders refinement of sampling methods. This study employed a fixed sampling array to explore how tidal phases affect the detection of Delta Smelt eDNA. Our primary objective was to estimate the effects of covariate metrics on concentration of eDNA (calculated as ln[eDNA]) observed in the tidal environment. Secondary objectives included comparing the effect of distance on eDNA concentration in the tidal system vs. a unidirectional system and estimating how time since species absence affects observed eDNA concentration. Model predictors that consistently affected eDNA concentration were distance from source, eddy diffusivity, time since species absence, tidal direction, and species. Distance had a consistently negative effect on eDNA concentration across both systems, though non-detections were more frequent in the tidal system than expected in a unidirectional one. Environmental DNA detections decreased over time, which suggests that positive eDNA detections from estuarine water sampling are more likely to co-occur contemporaneously with the actual presence of individuals. These findings improve the capacity to design sampling strategies that will detect target species within an estimated probability, if individuals are present within a specified distance. Enhanced detections using eDNA sampling approaches would refine determinations of if and when Delta Smelt are present at a location, which in turn lessens known information gaps related to species occurrence and distribution.
Although formalin is commonly used as a preserving reagent for tissue specimens, the fixation process itself damages DNA, which can be detrimental to most downstream genetic analyses. It may still be possible to confirm species identification from archived specimens by targeting short, species-specific genic regions. In this study we genetically verified maternal mitochondrial lineage from 150 hatchery larval Delta Smelt (Hypomesus transpacificus) that were preserved in 10% neutral, buffered formalin and Rose Bengal at room temperature (20–22 °C) for 611 days, 732 days, and 928 days. We targeted a region of the mitochondrial cytochrome b (Cyt-b) gene using a quantitative PCR (qPCR) assay designed to specifically amplify Delta Smelt environmental DNA (eDNA). Because mitochondrial genetic markers used for species identification are generally maternally inherited, detecting hybridization is not possible using species-specific mitochondrial markers if among-species hybrids are present. Because Delta Smelt can hybridize with non-native Wakasagi Smelt (Hypomesus nipponensis), we assumed in this study the method detected maternal lineage. Maternal mitochondrial lineage was confirmed in 100% of our 150 Delta Smelt samples analyzed, although the strength of detection appeared to decline over time. We posit that the short DNA target size (84 base pairs) of the Delta Smelt-specific qPCR assay allowed for successful identification, and we confirmed this by Sanger sequencing with the qPCR assay forward and reverse primers. Our results may be broadly applicable because formalin remains a commonly used fixative in the preservation of fish, reptiles, amphibians, and various invertebrate taxa. Additional testing with both Sanger- and Illumina-based sequencing methods on a subset of the larval extracts did not successfully produce positive identification.
The survival of juvenile Chinook Salmon (Oncorhynchus tshawytscha) depends on the specific migration route they take through the Sacramento–San Joaquin Delta. Factors such as flow magnitude, flow direction, and distribution of fish across the channel significantly affect the likelihood of their entering routes with lower survival probabilities. Management strategies to mitigate the entry of endangered winter-run and threatened spring-run Chinook Salmon into the interior Delta—particularly through Georgiana Slough—involve flow regulation and the installation of a bioacoustic fish fence. Monitoring the effectiveness of these measures has primarily relied on acoustically-tagged, juvenile, hatchery-reared, late-fall-run Chinook Salmon, which are easier to obtain and can accommodate larger tags compared to other runs. Previous studies explored how flow dynamics affect routing probabilities of late-fall-run Chinook Salmon, but there is a lack of understanding about how routing probabilities vary among runs. We leveraged data from 15 previous studies comprising 3,004 acoustically-tagged fish across all four runs, over a 12-year period, to assess the effects of run on routing probability into Georgiana Slough, while accounting for variation in flow dynamics. We employed logistic regression to model the influence of tidal flow metrics, time of day (day and night), and run type on the probability of juvenile Chinook Salmon being routed into Georgiana Slough. Our analysis revealed that reverse flow during incoming tides influenced the routing probabilities of all runs. An increased proportion of flow into Georgiana Slough, meant an increased probability for all runs to be routed into Georgiana Slough. Late-fall-run Chinook Salmon also showed a greater probability of routing into Georgiana Slough during the night than during the day, whereas the opposite was true for other runs. These differences in routing probability affect our understanding of how management actions intended to reduce routing into Georgiana Slough may differentially affect the four runs of Chinook Salmon in the Sacramento River.
Managing river–floodplain connectivity can be driven by environmental restoration and/or flood-risk objectives, and science programs are essential for informing projects and policies that promote both objectives. California’s Central Valley floodplains have been highly altered as the result of flow regulation, channelization, and levee construction. Much of the remaining floodplain-like habitats are within flood bypasses that are used to manage flood risk. In recent decades, the habitat value of these bypasses for native fishes has received increased attention, and in 2021 a symposium was held to share the results of over 20 years of scientific studies conducted on Central Valley floodplains and flood bypasses. The symposium sought to foster a shared understanding among scientists and managers about the current information on flood bypasses, and the remaining challenges that must be overcome to maximize benefits to native fish while managing trade-offs. This paper summarizes the symposium’s unique synthesis of the state of the science regarding benefits that native fish accrue from accessing flood bypasses, and remaining uncertainties about population-level benefits and risks when fish enter these systems. We describe a case study to demonstrate how restoration can be accomplished within the flood-bypass management context, provide examples of ongoing restoration projects in the Central Valley, and present recommendations for actions needed to manage and restore flood bypasses at a landscape-scale. Our summary identifies the need to develop a long-term vision for managing and restoring flood bypasses and floodplains throughout the valley that includes: quantifying fish population-level effects, identifying necessary funding sources to implement actions at a scale that achieves societal goals, and streamlining regulatory processes. These steps would allow the actions identified in the vision to be implemented in a transparent, consensus-driven, and timely manner.
We used acoustic telemetry to estimate survival of tagged release groups, and quantify differences between alternative hatchery release strategies. To assess whether offsite release could increase survival of hatchery fish relative to those released at the hatchery, we compare survival during emigration of hatchery fall Chinook Salmon (FCS, Oncorhynchus tshawytscha) smolts released onsite, at Coleman National Fish Hatchery (NFH), to those released at alternative offsite locations downstream in the upper Sacramento River, California. Approximately 300 fish in each release group were implanted with acoustic tags in the 3-year study during 2019, 2021, and 2022. Environmental conditions in the emigration corridor varied between study years, with extended high flows in 2019, whereas drought conditions and a flat hydrograph occurred in 2021 and 2022. Survival across years appeared to reflect environmental conditions, with higher overall survival seen in 2019. Survival differences between release sites generally showed higher cumulative survival to Knights Landing or Chipps Island for the downstream release groups, compared to the onsite releases during 2021 and 2022. This information suggests hatchery releases of FCS from Coleman NFH at downstream release sites may benefit emigration survival during years of drought and sub-optimal in-river conditions, compared to standard onsite releases. Hatchery managers can use information from this study to diversify the portfolio of release strategies, which may be useful to buffer against extreme variations of adult abundance by spreading risks across space and time. Ultimately, offsite releases may be a useful tool for adaptive management of these culturally, ecologically, and economically important salmon populations.
Deposition of inorganic sediment is essential for the sustainability of tidal salt marshes. Understanding variability in sediment sources and the processes of sediment delivery to salt marshes are high priorities for decision-makers responsible for managing sediment and conserving and restoring marshes. Research on sediment transport to marshes is published in technical journals, but these scientific findings must be translated and communicated to inform critical decisions related to managing sediment in estuaries. We convened a diverse group of collaborators—including natural-resource managers, regulators, scientists, and restoration planners and practitioners—to review and interpret the results of previously published field investigations on and around the salt marsh at China Camp State Park in Marin County, California. We discussed and translated key results of those studies using new graphics and more accessible language. Here, we present a general introduction to the topic of sediment delivery to salt marshes, background descriptions of the China Camp marsh and the physical processes that we characterized there, key scientific conclusions, and proposed management implications. Key conclusions include (1) bay shallows are an important but variable source of marsh sediment, (2) flood tides and waves move sediment across the bay–marsh edge, (3) tidal creeks may not always import sediment to the marsh platform, and (4) protective effects of marsh vegetation depend on species and season. China Camp marsh is one of the last remaining pre-colonial salt marshes in the San Francisco Estuary and is unique in being relatively unmodified by humans and in retaining an unimpeded transition into natural uplands. Additional studies in a variety of marshes with different attributes and sediment regimes will broaden understanding of how best to conserve, manage, and restore tidal marshes that provide numerous ecosystem services to for humans and wildlife.
Flooding in the Bay–Delta is most commonly due to runoff from atmospheric river (AR) storms, often enhanced by low-elevation snowmelt. In this paper, we review the current science of ARs and their projected enhancement in a warming climate. We also address the changing state of the Sierra Nevada snowpack. Climate-model projections indicate increasing contributions to extreme precipitation from ARs, and more variable hydroclimate, with increased floods as well as droughts. Observations, meanwhile, do not yet show enhanced precipitation intensity trends. In agreement with climate-model projections, observations do show that, as the climate continues to warm, California’s greatest natural freshwater reservoir—its snowpack—continues to erode. This is despite record snowpacks (e.g., 2023) still being possible, and potentially exacerbating flood effects from ARs in a highly variable hydroclimate. Original analysis of extreme historical and projected precipitation events shows the occurrence of the magnitude at the level associated with the New Year 1997 floods are expected to become twice as likely by the late 21st century. Moreover, as extreme precipitation events are expected to become wetter, hydrologic modeling suggests that extreme runoff events will be disproportionately enhanced, primarily as the result of a greater fraction of rain vs. snow. We also discuss the mitigating influence of water management on extreme flows, and mention new research results, challenges, and opportunities associated with sub-seasonal and seasonal precipitation predictability. We suggest that—along with infrastructural modernization, as well as maintenance and improvement of observational networks—current and future challenges for water management can be mitigated by better and longer lead-time weather and climate-forecast information.
California’s variable hydroclimate is projected to become increasingly volatile in the 21st century. Yet, there is widespread recognition that extreme events, such as record-breaking heatwaves and catastrophic wildfires, are already becoming the new normal. The 2025 edition of the State of Bay–Delta Science (SBDS) presents the current state of the science on climate change and extreme events affecting the Delta and its watershed, and in doing so, generates new insights on knowledge gaps and promising directions for future research. In this essay we present five perspectives on advancing the Delta scientific system to keep pace with climate change. The Delta has many effective scientific practices already in place, including long-term monitoring programs, collaborative synthesis venues, science-informed decision-making processes, and community partnerships. New and sophisticated tools that harness big data are helping to streamline information flows to researchers and decision-makers. Open science practices are facilitating greater collaboration and improving access to more integrated datasets and to models that link different parts of the system. These assets have strengthened innovation and learning across the Delta. Nevertheless, serious challenges remain. Climate change signals can be difficult to detect as a result of the variable hydroclimate. Higher levels of scientific uncertainty can present challenges for traditional decision-making processes. Looking forward, the Delta scientific system can help maintain its relevance to natural resource management by strengthening its capacity for collaborative, open, and actionable science. Such an emphasis is required for anticipating and responding to the new climate and weather realities of the 21st century.
Freshwater inflow is vital for the ecological health of estuaries. Understanding historical flow volume and timing is therefore essential for sustainable management and restoration of these environments. Using legacy hydrologic data—including riverine water-level measurements, watershed runoff estimates, and wetland reclamation records—we extended a monthly time-series of freshwater inflow to San Francisco Estuary by 6 decades, back to California’s Gold Rush era. This period marks the onset of significant anthropogenic modifications to the waterscape. Our analysis of the extended series, normalized to unimpaired runoff, reveals an increasing trend in systemwide water use that was preceded by a decline in the latter half of the 19th century. We hypothesize this decline resulted from reduced evapotranspiration as a result of vegetation removal and reduced overbank flows from levee construction. These findings align with earlier research that shows similarities between natural and contemporary long-term annual average inflow, comparing pre-development conditions to those of the early 20th century and today. Monthly flow trends, however, displayed more nuanced, season-specific effects of human modifications. Despite unusually wet hydrology during the reconstruction period, our findings comprise an important contribution to ongoing dialogue on ecosystem-restoration targets.
Fish losses to entrainment in water diversions in the Sacramento–San Joaquin Delta have been a long-standing conservation concern. We evaluated Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys) entrainment risk associated with the Barker Slough Pumping Plant (BSPP) by integrating hydrodynamic, growth, survival, and fish-screen-selectivity information into indices of entrainment risk for nine locations in the Cache Slough Complex (CSC). Our fundamental question was: How does risk of entrainment into BSPP vary in space and time? We found the predicted risk of entrainment into BSPP is extremely high from the adjacent Lindsey Slough. From elsewhere in the CSC, entrainment risk into BSPP is approximately zero in both wet and dry years, such that local irrigation diversions are the only potential source of entrainment loss. We estimated Delta Smelt outgrow vulnerability to entrainment through the BSPP fish-screens in 35 to 53 days while Longfin Smelt remain vulnerable for 90 to 98 days. Research indicates some impingement is probable even after fish outgrow risk of being entrained through the screens if they continue to be passively transported. Our entrainment indices sometimes deviated considerably from hydrodynamic transport predictions within Lindsey Slough because larval fish have high natural mortality rates and, at least for Delta Smelt, growth rates high enough to modify the transport predictions. Since 1989, the predicted entrainment risk at BSPP has declined in the winter but increased in April through May as a result of long-term trends in how much water is seasonally diverted at BSPP. If the one-dimensional model we used to estimate fish transport is accurate, then Delta Smelt and Longfin Smelt would need to be spawned in Barker or Lindsey sloughs to face a meaningful risk of entrainment at BSPP. This conclusion does not appear to be affected by Yolo Bypass flow as had been hypothesized previously.
Global change affects the forests and wildlands of California through rising temperatures, earlier snowmelt, more rain and less snow, greater vapor-pressure deficits, and forest dieback, resulting in increased wildfire frequency, size, and severity. California has experienced its eight largest wildfires since 1932 in the period from 2018 to 2024. The largest fire to date (August Complex Fire) occurred in 2020 and burned 418,000 ha, a year in which 1.7 million ha or 4% of California’s land area burned. These mega-fires (>10,000 ha) have the potential to cause severe effects on water quality and aquatic ecosystems. Water-quality variables affected by wildfire include temperature, sediment load, turbidity, dissolved oxygen, pH, redox potential, soluble and particulate organic carbon, nutrients, metals, natural- and human-produced organic contaminants, and primary/secondary producers. Wildfire and water interact at watershed scales, with water-quality impairments responding linearly with the percentage of the watershed area burned, and responding exponentially as burn severity increases. Vegetation recovery is key to the duration of water-quality effects, and short-term, post-fire weather dictates actual water-related effects. Urban areas are hot spots for the production and transport of water pollutants such as sediments, heavy metals, mercury, nutrients, and toxic organic compounds. Water-treatability challenges after wildfire include short-term odor and taste, increased sediment and turbidity, and increased total and dissolved organic matter. Implications for water quality from catastrophic wildfire on downstream reservoirs are important research needs because ~80% of California’s water supply passes through reservoirs before use. Notably, there is a crucial need for development and assessment of post-fire, land-management practices to mitigate adverse water-quality effects. Finally, continuous measurements of water quality are critical to document the severity and duration of episodic pulses of wildfire-sensitive constituents that are mobilized and transported to aquatic ecosystems after catastrophic mega-fires.
The restoration of native species-dominated ecosystems is critical for improving ecosystem health and meeting policy goals in the Sacramento–San Joaquin Delta and Suisun Marsh (upper San Francisco Estuary, collectively), one of the largest estuarine systems in North America. To accomplish large-scale restoration in this heavily altered system, a variety of projects, programs, and motivations inform restoration planning and implementation. Chapter 4, “Ecosystem,” of the Delta Plan synthesizes restoration goals across these efforts to produce comprehensive ecosystem restoration targets of between 60,000 and 80,000 acres across seven ecosystem types by 2050, but a comprehensive review of restoration progress and planning to date is needed. To fill this gap, this paper analyzes the current state of ecosystem restoration in the upper San Francisco Estuary in the context of the Delta Plan targets. We review current scientific and management literature and implementation approaches, and synthesize acreage totals across completed, in-progress, and planned projects for four ecosystem types where substantial development of restoration in the system has occurred: tidal wetland, non-tidal wetland, riparian, and floodplain. We find that tidal wetland restoration has progressed more rapidly than other ecosystem types, motivated by mitigation requirements related to the federal Endangered Species Act. Across all ecosystem types, we identify both promising progress and clear needs for accelerated planning and implementation of restoration projects to meet Delta Plan 2050 targets, and discuss ongoing needs related to science, funding, and implementation.
Zooplankton are a key food source for juvenile fishes in estuaries worldwide, including California’s Sacramento–San Joaquin Delta (hereafter Delta); both zooplankton quality and quantity are critical to ecosystem health. Zooplankton may be affected by pesticides in water and the food web, and the Delta is known to contain complex pesticide mixtures. In this study, we evaluated pesticide concentrations in water and zooplankton in the northern Delta during (1) the summer–fall of 2017, 2018, and 2019, which included periods of augmented pulse flows from agriculture tailwater, and (2) across a full seasonal cycle from May 2019 to March 2020. We quantified changes in pesticide concentration in response to environmental factors. We found that zooplankton showed more frequent detections of hydrophobic pesticides compared to more frequent detections of hydrophilic compounds in water. Pesticide concentrations were influenced by flow, pesticide application, and season, but the effects of these environmental factors differed by habitat (Sacramento River or Yolo Bypass Toe Drain). Pesticides in water responded similarly to environmental factors in the Sacramento River and Yolo Bypass, whereas pesticides in zooplankton responded differently. In water, we found more detections and higher concentrations at higher flows in the Yolo Bypass and Sacramento River, but responses to pesticide application varied by habitat. Alternatively, pesticide concentrations in zooplankton increased in the Yolo Bypass with increasing flow (correlated with flow pulses) and changed seasonally; whereas, pesticide concentrations in zooplankton in the Sacramento River decreased at higher flows, and decreased with or did not respond to higher pesticide application in the watershed. Our study suggests that augmented flows—particularly those using agricultural tailwater—may have unintended negative ecological effects that could partially offset benefits to the food web and fishes in the northern Delta, underscoring the complex interplay among factors that drive increased pesticide exposure.
Strategies for endangered species conservation may have different outcomes depending on the habitat context in which they are implemented. Understanding these context-dependent effects can help optimize and target management efforts. In this analysis, we investigate how environmental and food-web conditions interactively affect condition and foraging of Delta Smelt (Hypomesus transpacificus), an endangered fish endemic to the San Francisco Estuary (the estuary). Food limitation, in terms of pelagic zooplankton availability, is considered a main factor that contributes to the decline in Delta Smelt abundance. Our overarching objective was to examine whether the effect of zooplankton on Delta Smelt depended on habitat context. Specifically, we hypothesized that zooplankton would less positively affect Delta Smelt condition—as measured by hepatosomatic index (HSI)—and foraging success in areas with nearby tidal wetlands, because these adjacent habitats may provide access to prey items from the epibenthos and fringing vegetation. In contrast, in regions with limited proximity to wetlands, we hypothesized that Delta Smelt would rely more on pelagic prey, which would manifest as a more positive effect of zooplankton on body condition and foraging success for Delta Smelt. Using models that accounted for habitat in multiple ways, we found little evidence that zooplankton and habitat interactively influenced Delta Smelt condition or gut fullness. Rather, the influence of zooplankton on HSI and gut fullness was generally positive across habitat contexts. Given the well-documented food limitation in the estuary, promoting the availability of pelagic zooplankton is a rational, albeit complex, management aim. Furthermore, our results suggest that efforts to increase zooplankton would broadly benefit Delta Smelt across a wide range of habitat contexts.
Most managed wetlands in California are ephemeral and are purposefully flooded during the fall and winter for over-wintering waterfowl, and are dry during the spring and summer waterfowl breeding season. Only semi-permanent and permanent wetlands remain flooded through the critical summer brood-rearing period for ducklings. We examined the availability of flooded wetlands for breeding waterfowl in the brackish Suisun Marsh (California, USA) annually during the spring (April 27–May 17, during peak nesting) and summer (June 17–July 7, during peak duckling brood rearing), for a 38-year period using Landsat satellite imagery and spectral mixture analysis. Flooded wetland area increased 43% in spring and 48% in summer from 1984 to 2021 but varied among years (spring: 37.6–88.6 km2; summer: 17.7–57.5 km2). This increase in flooded wetland area over the past 4 decades was due to just a few sites, with only 24% (spring) and 15% (summer) of the 198 land-owner parcels increasing in flooded area. Flooded wetland area in the spring was unrelated to annual precipitation between October and April (range: 25–104 cm) or spring precipitation between January and April (range: 8–65 cm), whereas flooded wetland area in the summer was weakly correlated to both annual and spring precipitation. Flooded wetland area in spring and summer was also weakly correlated with the median daily outflow from the Sacramento–San Joaquin River Delta between March 15 and June 15, which corresponds to a critical period of wetland water management for breeding waterfowl. Our results indicate that spring and summer flooded wetland habitat for breeding waterfowl has increased slightly over the past 4 decades, varies annually, and mostly depends on local wetland management practices rather than on precipitation or Delta outflow. Managing habitats as semi-permanent wetlands would increase flooded wetland habitat in the spring and summer, and provide habitat for nesting hens and ducklings.
Sediment bulk density (ρdry) and particle size are two important parameters for predicting sediment bed erosion. ρdry, however, is difficult to measure accurately. The units of ρdry have not been consistently reported in the literature, leading to confusion, particularly in the calculation of sediment budgets that typically require integrating mass-based and volumetric components. Relationships between ρdry and sediment composition have been developed for multiple regions and differ between systems. Developing a system-specific predictive model for ρdry can help fill data gaps and improve sediment budgets, model accuracy, and estimates of quantities of sediment needed for restoration. In this study, we investigate whether ρdry in San Francisco Estuary can be predicted from organic carbon content or percent of fines, which are more easily or frequently measured than ρdry. We compiled sediment properties from samples collected over the past decade throughout the intertidal and subtidal regions of San Francisco Bay and the Sacramento–San Joaquin Delta to examine this relationship. Sample composition ranged from 2.18 to 99.97% fines (particles < 0.0625 mm), ρdry ranged from 0.22 to 1.60 g cm –3, and organic carbon ranged from 0.06 to 7.98%. Regression analysis indicates that the percent of fines explains 93% of the variation of ρdry (p-value < 0.05, N = 81). The coefficient of determination decreased by ~1% when organic carbon was incorporated in the regression analysis. Comparison of this predictive ρdry model to four published models based on samples from other regions supports previous findings that the relationship between ρdry and particle size may vary by system. We also examined additional factors that may affect sediment erodibility, such as hydrographic and oceanographic conditions. Classification of sample sites as intertidal vs. subtidal or wavy vs. non-wavy each significantly explained the residuals from the ρdry model, and both intertidal and wavy conditions were associated with higher ρdry values.
Sacramento River winter-run Chinook Salmon (Oncorhynchus tshawytscha) are an endangered population that faces numerous challenges across its life cycle, including juvenile out-migration through the heavily anthropogenically modified Sacramento–San Joaquin Delta, or Delta. Water exports from pumping facilities in the Delta can alter local hydrology and influence movement of out-migrating juveniles, some of which are observed in or near pumping facilities. Monitoring and regulations, intended to protect out-migrating fish through restrictions on pumping, are predicated on assumed relationships among fish observations, water operations, and through-Delta migratory survival. In this study, we use a new conceptual model to review the current state of science for winter-run Chinook Salmon out-migration survival in the Delta, and use simulation modeling to address pertinent knowledge gaps. Results of this study highlight varying support for the influence of Sacramento River flow, temperature, and water exports on routing and survival in different regions of the Delta. The contributions of specific routing pathways to the interior Delta (e.g., through Threemile Slough) to survival, and the relationship between fish entrainment at pumping facilities and overall migratory survival, remain uncertain. Recommended future work includes continued fine-scale acoustic telemetry studies throughout the Delta, novel integrated modeling of monitoring data, and contextualizing the relevance of Delta-based survival to population viability by incorporating explicit uncertainties about survival into existing life-cycle models.
