San Francisco Estuary and Watershed Science

Management of the Sacramento River and Sacramento–San Joaquin Delta (SRD) is one of California’s greatest challenges, requiring trade-offs between valued components that serve a multiplicity of conflicting purposes. Trade-offs do not signal a failure to create clever enough models, or scenarios that find a single optimal solution. Rather, an optimal solution that meets multiple objectives does not exist. We demonstrate an improved method for multiple-objective allocation of water: “turn-taking” optimization (TTO) within a multi-model cloud computing framework. We apply TTO to an array of physical hydrologic models that are linked with the Ecological Flows Tool (EFT): a multi-species decision support framework to evaluate how specific components of the flow regime promote and balance favorable habitat conditions for 15 representative species and 31 indicators within the SRD. Applying the TTO approach incorporates the existing modelled representation of socio-economic water management criteria, priorities, and constraints — and optimizes water-release patterns each water year using a dynamically shifting set of EFT indicators. Rather than attempting to optimize conditions for all ecological indicators every year, TTO creates flexibility and opportunities for different indicators to be successful in different years, informed by the frequency with which each species’ ecological needs should be met. As an individual EFT indicator is successful in a particular year, its priority in one or more subsequent years is reduced (and vice versa). Comparing TTO to a Reference Case scenario based on current management practices, 12 EFT indicators are improved, 14 show no change, and 5 show a reduction in suitability. When grouped into nine species and life-history groups, performance improved in four (late-fall-run Chinook, winter-run Chinook, spring-run Chinook, and Fremont cottonwood), did not change in four (fall-run Chinook Salmon, Delta Smelt, Splittail, and Longfin Smelt), and was worse in one group (Steelhead).

Although brackish marsh has been the subject of decades of research, tidal freshwater regions are still poorly understood. To provide insight into spatial and temporal dynamics of nutrients, physical conditions, and the plankton community in freshwater tidal habitat, we investigated from 2011 to 2014 a remnant freshwater tidal slough complex located in the Sacramento–San Joaquin Delta region of the San Francisco Estuary. Our results suggest that the tidal slough complex showed different seasonal nutrient, physical, and biological conditions when compared to a relatively homogenous adjacent large river channel, the Sacramento River. The tidal slough complex also showed substantial spatial variability in habitat conditions compared to nearby main river channels. Nutrient dynamics in the tidal slough complex appear to be driven by a complex suite of factors, including inflow from upstream tributaries and tidal flows from the downstream reach of the Sacramento River. Chlorophyll a in the tidal sloughs responded more strongly to upstream flow pulses than other environmental variables. The tidal slough complex generated significantly higher levels of chlorophyll a than other freshwater regions of the Delta. The 2011 and 2012 results were especially notable because unusually large flow pulses through the tidal slough complex appear to have contributed to rare phytoplankton blooms in downstream areas of the Delta during the fall months. Moreover, the 2012 flow pulse stimulated higher trophic levels, because significantly higher levels of zooplankton were in the tidal slough complex after the flow event. These results have important implications for our understanding of the functioning of freshwater tidal habitat, and for the design of potential restoration projects in these regions.

Central Valley spring-run Chinook Salmon (CVSC) are designated threatened by state and federal authorities. Although CVSC are caught in ocean fisheries, their harvest is not actively managed, because it is assumed that measures currently in place to protect endangered Sacramento River winter-run Chinook Salmon (SWRC) will also sufficiently protect CVSC. Recoveries of tags and genetically-identified CVSC suggest these fish have a more northerly distribution than SRWC. Further, escapement data and cohort reconstructions suggest that CVSC mature later than SRWC. Thus, regulations (time/area restrictions and minimum size limits) crafted to protect SRWC alone may not adequately protect CVSC; on the other hand, regulations to constrain impacts on Klamath River and California coastal Chinook Salmon populations may also reduce impacts on CVSC. Trends in CVSC escapement were deemed acceptable in recent status updates, but concerns remain because of the negative effects caused by recent drought and ocean conditions. Should more active management of CVC be desired, current options are limited. The most promising approach is based on estimating age-specific ocean fishing mortality rates by using cohort reconstructions applied to tagged Chinook Salmon that originate from the Feather River Hatchery. At a minimum, ocean fishing mortality rates could be monitored and compared to proxy thresholds. If reference harvest rates were established, harvest models could be developed to predict how CVSC would be affected by fishing regulations, similar to the way fall-run Chinook Salmon fisheries are evaluated. Abundance forecasts would require improved juvenile production data (e.g., from genetic sampling of juvenile emigrants), since sibling-based forecasts commonly used for fall-run Chinook Salmon would not be available in time for pre-season planning. It is unclear if ocean fishing mortality rate estimates derived from hatchery proxies for natural-origin fish are truly representative, but existing data do not demonstrate obvious differences in ocean distribution or size-at-age fish. Substantial new investments in tagging or sampling would be needed to directly estimate ocean fishing mortality rates for natural-origin CVSC. Establishing specific harvest targets or limits for CVSC requires an improved understanding of production throughout their life cycle through juvenile production estimates and long-term information on spawner age structure.