San Francisco Estuary and Watershed Science

This paper reviews environmental management and the use of science in the Sacramento–San Joaquin Delta during California’s 2012–2016 drought. The review is based on available reports and data, and guided by discussions with 27 agency staff, stake-holders, and researchers. Key management actions for the drought are discussed relative to four major drought water management priorities stated by water managers: support public health and safety, control saltwater intrusion, preserve cold water in Shasta Reservoir, and maintain minimum protections for endangered species. Despite some success in streamlining communication through interagency task forces, conflicting management mandates sometimes led to confusion about priorities and actions during the drought (i.e., water delivery, the environment, etc.). This report highlights several lessons and offers suggestions to improve management for future droughts. Recommendations include use of pre-drought warnings, timely drought declarations, improved transparency and useful documentation, better scientific preparation, development of a Delta drought management plan (including preparing for salinity barriers), and improved water accounting. Finally, better environmental outcomes occur when resources are applied to improving habitat and bolstering populations of native species during inter-drought periods, well before stressful conditions occur.

Biological invasion by non-native species has been identified as one of the major threats to native fish communities worldwide. The fish community of San Francisco Estuary is no exception, as the estuary has been recognized as one of the most invaded on the planet and the system has been impacted significantly by these invasions. Here, we summarize the introduction and probable establishment of a new species in the Sacramento–San Joaquin Delta, the Bluefin Killifish (Lucania goodei), as discovered by the US Fish and Wildlife Service Delta Juvenile Fish Monitoring Program (DJFMP). The DJFMP has conducted a large-scale beach seine survey since 1976, and it is the longest-running monitoring program in the San Francisco Estuary that extensively monitors the shallow-water nearshore habitat. Possibly introduced as discarded aquarium fish within the vicinity of the Delta Cross Channel, Bluefin Killifish is a close relative of the Rainwater Killifish (Lucania parva), another non-native fish species that has been present in the San Francisco Estuary system for decades. Studies in their native range suggest that Bluefin Killifish will fill a similar niche to Rainwater Killifish, albeit with a more freshwater distribution. The potential ecological impact of Bluefin Killifish remains unclear in the absence of additional studies. However, we have been able to track the spread of the species within the Sacramento–San Joaquin Delta through the existence of long-term monitoring programs. Our findings demonstrate the value of monitoring across various habitats for the early detection and proactive management of invasive species.

Many fishes in the San Francisco Estuary have suffered declines in recent decades, as shown by numerous long-term monitoring programs. A long-term monitoring program, such as the Interagency Ecological Program, comprises a suite of surveys, each conducted by a state or federal agency or academic institution. These types of programs have produced rich data sets that are useful for tracking species trends over time. Problems arise from drawing conclusions based on one or few surveys because each survey samples a different subset of species or reflects different spatial or temporal trends in abundance. The challenges in using data sets from these surveys for comparative purposes stem from methodological differences, magnitude of data, incompatible data formats, and end-user preference for familiar surveys. To improve the utility of these data sets and encourage multi-survey analyses, we quantitatively rate these surveys based on their ability to represent species trends, present a methodology for integrating long-term data sets, and provide examples that highlight the importance of expanded analyses. We identify areas and species that are under-sampled, and compare fish salvage data from large water export facilities with survey data. Our analysis indicates that while surveys are redundant for some species, no two surveys are completely duplicative. Differing trends become evident when considering individual and aggregate survey data, because they imply spatial, seasonal, or gear-dependent catch. Our quantitative ratings and integrated data set allow for improved and better-informed comparisons of species trends across surveys, while highlighting the importance of the current array of sampling methodologies.

Spawn timing in anadromous Pacific salmon may be especially sensitive to environmental cues such as river temperature and flow regimes. In this study, we explored correlations between peak spawn timing and water temperature in endangered Sacramento River winter-run Chinook Salmon. In recent drought years, rising water temperatures during egg incubation have negatively affected the winter-run Chinook Salmon population. This paper seeks to understand how winter-run spawn timing may be affected by temperatures during the staging period prior to spawning, and how water releases from Shasta Dam might affect these dynamics. We fit a proportional-odds logistic regression model to evaluate annual spawn timing as a function of average temperatures in April and May below Keswick Dam. While the start date of spawning remains relatively constant from year to year, the timing of peak spawning varies annually. Cool springtime temperatures trigger winter-run Chinook Salmon to spawn earlier, whereas warm springtime temperatures trigger fish to spawn later. Before dam construction, winter-run Chinook Salmon spawned in cool, spring-fed streams that are now inaccessible to migrating salmonids. In their natal spawning grounds, temperature-driven spawn timing would have primarily ensured sufficient time for egg maturation in cool years, while secondarily preventing egg and alevin mortality in warm years. In the current winter-run spawning grounds, the relationship between temperature and spawn timing may have important applications to management of Shasta Dam water releases, especially during conditions when thermal mortality can affect developing winter-run Chinook Salmon eggs.