Out-migration survival of wild Chinook salmon (Oncorhynchus tshawytscha) smolts from Mill Creek through the Sacramento River during drought conditions

Once emerged from the gravel after being spawned in natal streams, Chinook salmon spend many months rearing and growing in freshwater before undergoing smoltification and out-migrating to the ocean. This relatively short period of time is considered to be the most vulnerable and dangerous phase in the life cycle of a Pacific salmon. It is during this phase when smolts navigate around many anthropogenic structures and experience environmental stressors while making their way to the ocean. In California’s Central Valley, the few remaining wild populations of Chinook salmon (Oncorhynchus tshawytscha) out-migrate through a highly modified riverine and estuary landscape characterized by leveed banks, altered flow and temperature regimes, transformed food webs, and limited floodplain and rearing habitat. Juvenile salmon smolts migrate through these landscapes within a relatively short period of time, requiring them to quickly adapt to changing water conditions and habitat types. Understanding the survival rates of wild smolts from source tributaries to the Pacific Ocean is essential in protecting and restoring these populations from the low abundances currently observed. When faced with drought conditions out-migrating smolts experience low flows, elevated water temperatures and high densities of predators while out-migrating to sea. In order to assess smolt survival during drought conditions in late spring (April-May), 304 wild smolts were acoustically tagged and tracked from Mill Creek (Tehama County) to the Pacific Ocean between 2013 and 2016. Total outmigration survival to the ocean was 0.3% during these years, with only one fish making it to the Golden Gate and the Pacific Ocean. These survival estimates are some of the lowest ever recorded for salmon out-migrating to the Pacific Ocean, with much of the mortality occurring within Mill Creek and the Sacramento River. Cumulative survival through Mill Creek (rkm 452-441) was 68% (±12 S.E.), and cumulative survival through the Sacramento River (rkm 441-203) was 7.6% (± 16 S.E.) These low survival rates are likely attributed to low flows in Mill Creek and the Sacramento River resulting from critically dry winters between 2013 and 2015, which were reduced even further by water diversions for agriculture in both Mill Creek and the Sacramento River. During periods of higher flow in 2016 survival rates dramatically increased, suggesting that more water in Mill Creek and the Sacramento River is necessary to improve in-river smolt migration survival during the late spring

Out-migration survival of wild Chinook salmon (Oncorhynchus tshawytscha) smolts from Mill Creek through the Sacramento River during drought conditions

Once emerged from the gravel after being spawned in natal streams, Chinook salmon spend many months rearing and growing in freshwater before undergoing smoltification and out-migrating to the ocean. This relatively short period of time is considered to be the most vulnerable and dangerous phase in the life cycle of a Pacific salmon. It is during this phase when smolts navigate around many anthropogenic structures and experience environmental stressors while making their way to the ocean. In California’s Central Valley, the few remaining wild populations of Chinook salmon (Oncorhynchus tshawytscha) out-migrate through a highly modified riverine and estuary landscape characterized by leveed banks, altered flow and temperature regimes, transformed food webs, and limited floodplain and rearing habitat. Juvenile salmon smolts migrate through these landscapes within a relatively short period of time, requiring them to quickly adapt to changing water conditions and habitat types. Understanding the survival rates of wild smolts from source tributaries to the Pacific Ocean is essential in protecting and restoring these populations from the low abundances currently observed. When faced with drought conditions out-migrating smolts experience low flows, elevated water temperatures and high densities of predators while out-migrating to sea. In order to assess smolt survival during drought conditions in late spring (April-May), 304 wild smolts were acoustically tagged and tracked from Mill Creek (Tehama County) to the Pacific Ocean between 2013 and 2016. Total outmigration survival to the ocean was 0.3% during these years, with only one fish making it to the Golden Gate and the Pacific Ocean. These survival estimates are some of the lowest ever recorded for salmon out-migrating to the Pacific Ocean, with much of the mortality occurring within Mill Creek and the Sacramento River. Cumulative survival through Mill Creek (rkm 452-441) was 68% (±12 S.E.), and cumulative survival through the Sacramento River (rkm 441-203) was 7.6% (± 16 S.E.) These low survival rates are likely attributed to low flows in Mill Creek and the Sacramento River resulting from critically dry winters between 2013 and 2015, which were reduced even further by water diversions for agriculture in both Mill Creek and the Sacramento River. During periods of higher flow in 2016 survival rates dramatically increased, suggesting that more water in Mill Creek and the Sacramento River is necessary to improve in-river smolt migration survival during the late spring

Concurrent Sessions C: Fish Screening at Water Diversions I - Predator Densities And Associated Salmonid Smolt Mortality Around Water Diversions

State-of-the-art fish screens on large water diversions effectively prevent juvenile salmon from being entrained by the diversion, but the physical structure and their prey-concentrating effect may attract predators and create a local predation problem. We are assessing the impact of predation near two large diversions on juvenile Central Valley Chinook salmon (Oncorhynchus tshawytscha) using a combination of acoustic telemetry, a DIDSON camera, and tethering. We expect to answer these questions: (1) Is predator density higher near water diversions relative to nearby areas?(2) Do predators express site fidelity to the diversions?(3) Is the relative smolt predation rate near the diversions higher than nearby areas? What about seasonal and diel predation rate dynamics?(4) What proportion of the predators’ diets consists of smolts near the diversions?(5) All factors combined, does this result in higher than average smolt mortality rates near the diversions?During a pilot season in 2011 on one diversion on the Sacramento River, we gained limited insight into these questions. Predator densities were lowest near the diversion, and highest near the riverbank. Striped bass (Morone saxatilis) did not seem to express site fidelity while Sacramento pikeminnow (Ptychocheilus grandis) did. Finally, relative predation rates around the diversion were near average, with the highest relative predation rates near the riverbank. In the 2012 season, we added a second diversion representing a different design model, allowing the comparison of predator-prey dynamics between different commonly-used diversion designs. We will present data from this more intensive second season along with a preliminary look at data from the 2013 season. This project was conceived in response to the knowledge gap regarding how large water diversions influence predator-smolt dynamics; the majority of research on the impacts of diversions on salmonids concentrate on dewatering and lethal entrainment into pump

Concurrent Sessions C: Fish Screening at Water Diversions I - Predator Densities And Associated Salmonid Smolt Mortality Around Water Diversions

State-of-the-art fish screens on large water diversions effectively prevent juvenile salmon from being entrained by the diversion, but the physical structure and their prey-concentrating effect may attract predators and create a local predation problem. We are assessing the impact of predation near two large diversions on juvenile Central Valley Chinook salmon (Oncorhynchus tshawytscha) using a combination of acoustic telemetry, a DIDSON camera, and tethering. We expect to answer these questions: (1) Is predator density higher near water diversions relative to nearby areas?(2) Do predators express site fidelity to the diversions?(3) Is the relative smolt predation rate near the diversions higher than nearby areas? What about seasonal and diel predation rate dynamics?(4) What proportion of the predators’ diets consists of smolts near the diversions?(5) All factors combined, does this result in higher than average smolt mortality rates near the diversions?During a pilot season in 2011 on one diversion on the Sacramento River, we gained limited insight into these questions. Predator densities were lowest near the diversion, and highest near the riverbank. Striped bass (Morone saxatilis) did not seem to express site fidelity while Sacramento pikeminnow (Ptychocheilus grandis) did. Finally, relative predation rates around the diversion were near average, with the highest relative predation rates near the riverbank. In the 2012 season, we added a second diversion representing a different design model, allowing the comparison of predator-prey dynamics between different commonly-used diversion designs. We will present data from this more intensive second season along with a preliminary look at data from the 2013 season. This project was conceived in response to the knowledge gap regarding how large water diversions influence predator-smolt dynamics; the majority of research on the impacts of diversions on salmonids concentrate on dewatering and lethal entrainment into pump

Nonlinear survival of imperiled fish informs managed flows in a highly modified river

Abstract Water is a fundamental resource in freshwater ecosystems, and streamflow plays a pivotal role in driving riverine ecology and biodiversity. Ecologically functional flows, managed hydrographs that are meant to reproduce the primary components of the natural hydrograph, are touted as a potential way forward to restore ecological functions of highly modified rivers, while also balancing human water needs. A major challenge in implementing functional flows will be establishing the shape of the managed hydrograph so as to optimize improvements to the ecosystem given the limited resources. Identifying the shape of the flow–biology relationship is thus critical for determining the environmental consequences of flow regulation. In California's Central Valley, studies have found that increased streamflow can improve survival of imperiled juvenile salmon populations during their oceanward migration. These studies have not explored the potential nonlinearities between flow and survival, giving resource managers the difficult task of designing flows intended to help salmon without clear guidance on flow targets. We used an information theoretic approach to analyze migration survival data from 2436 acoustic‐tagged juvenile Chinook salmon from studies spanning differing water years (2013–2019) to extract actionable information on the flow–survival relationship. This relationship was best described by a step function, with three flow thresholds that we defined as minimum (4259 cfs), historic mean (10,712 cfs), and high (22,872 cfs). Survival varied by flow threshold: 3.0% below minimum, 18.9% between minimum and historic mean, 50.8% between historic mean and high, and 35.3% above high. We used these thresholds to design alternative hydrographs over the same years that included an important component of functional flows: spring pulse flows. We compared predicted cohort migration survival between actual and alternative hydrographs. Managed hydrographs with pulse flows that targeted high survival thresholds were predicted to increase annual cohort migration survival by 55–132% without any additions to the water budget and by 79–330% with a modest addition to the water budget. These quantitative estimates of the biological consequences of different flow thresholds provide resource managers with critical information for designing functional flow regimes that benefit salmon in California's highly constrained water management arena

Considerations for the Development of a Juvenile Production Estimate for Central Valley Spring-Run Chinook Salmon

Effective species management depends on accurate estimates of population size. There are, however, no estimates of annual juvenile production for Central Valley spring-run Chinook Salmon (“spring run”), a highly imperiled species in California, making it difficult to evaluate population status and effectively manage key issues such as entrainment of this species at water diversions. In recognition of this critical information gap, we initiated an effort to develop a juvenile production estimate (JPE) for spring run, defined here as an annual forecast of the number of juvenile Central Valley spring-run Chinook Salmon that enter the Sacramento–San Joaquin Delta (“Delta”) from the Sacramento Valley. This metric would allow for a more robust scientific assessment of the population, which is needed to effectively manage water to reduce effects on spring run, a key condition of state permit requirements. To help guide this effort, we organized a workshop for stake-holders, managers, and scientists to review some of the key aspects of spring-run biology, examine the management and conservation importance of a JPE, identify knowledge gaps, introduce new tools, and discuss alternative approaches to forecasting the number of spring run emigrating from the Sacramento River drainage and into the Delta. This paper summarizes the spring-run biology, monitoring, and emergent methods for assessment considered at the workshop, as well as the guiding concepts identified by workshop participants necessary to develop a JPE for spring-run Chinook Salmon