Populations of wild spring-run Chinook salmon in California's Central Valley, once numbering in the millions, have dramatically declined to record low numbers. Dam construction, habitat degradation, and altered flow regimes have all contributed to depress populations, which currently persist in only a few tributaries to the Sacramento River. Mill Creek (Tehama County) continues to support these threatened fish, and contains some of the most pristine spawning and rearing habitat available in the Central Valley. Despite this pristine habitat, the number of Chinook salmon returning to spawn has declined to record low numbers, likely due to poor outmigration survival rates. From 2013 to 2017, 334 smolts were captured and acoustic tagged while outmigrating from Mill Creek, allowing for movement and survival rates to be tracked over 250 km through the Sacramento River. During this study California experienced both a historic drought and record rainfall, resulting in dramatic fluctuations in year-to-year river flow and water temperature. Cumulative survival of tagged smolts from Mill Creek through the Sacramento River was 9.5% (±1.6) during the study, with relatively low survival during historic drought conditions in 2015 (4.9% ± 1.6) followed by increased survival during high flows in 2017 (42.3% ± 9.1). Survival in Mill Creek and the Sacramento River was modeled over a range of flow values, which indicated that higher flows in each region result in increased survival rates. Survival estimates gathered in this study can help focus management and restoration actions over a relatively long migration corridor to specific regions of low survival, and provide guidance for management actions in the Sacramento River aimed at restoring populations of threatened Central Valley spring-run Chinook salmon.

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)(2014)(2015)(2016)(2017)(2018)(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.

California's Central Valley (CCV) Chinook Salmon Oncorhynchus tshawytscha stocks have declined substantially since the mid‐1800s, with most listed as threatened or endangered or heavily supplemented by hatcheries. As the largest population of CCV wild spring‐run Chinook Salmon, Butte Creek fish are an important source for promoting life history diversity in the CCV Chinook Salmon community. However, little information exists on Butte Creek juvenile mortality during out‐migration to the ocean, which is considered a critical phase in the overall population dynamics. We used the Juvenile Salmon Acoustic Telemetry System to track the movement of individual fish, and we used a mark–recapture modeling framework to estimate survival of migrating wild Chinook Salmon smolts from lower Butte Creek to ocean entry at the Golden Gate Bridge. Survival and migration varied significantly among years; in 2015, which was a dry year, Chinook Salmon smolts migrated more slowly throughout their migratory corridor and exhibited lower survival than in a wetter year (2016); among locations, fish migrated faster and experienced higher survival in the lower Sacramento River than in the Sutter Bypass and the Sacramento–San Joaquin River Delta. Our data suggest that higher flow at release and larger fish lengths both resulted in increased survival. Our findings shed light on a critical phase of wild spring‐run juvenile Chinook Salmon dynamics and could help to inform future restoration and management projects that would improve the survival and abundance of the CCV spring‐run Chinook Salmon populations.