San Francisco Estuary and Watershed Science

The Delta Plan (DSC 2013) calls for “protecting and enhancing the unique cultural values” of California’s Sacramento–San Joaquin Delta, a 2,800-km² (1,100 mi²) region that was occupied by indigenous peoples for ~5,000 years. The legacies of Native Californians need to be included in the Delta Plan, especially Traditional Ecological Knowledge (TEK) of ways to gather, hunt, and fish for food; build shelters; prepare medicines; and perform ceremonies — along with ways to make tools, clothing, baskets, and shelters. Plants were not just collected but also tended, which involved planned burning, digging, planting, weeding, harvesting, and seed dispersal. Populations of plants that have cultural significance and unique values should be enhanced under the Delta Plan. While Western Ecological Knowledge (WEK) offers a strong foundation for restoration of species assemblages and ecosystems, TEK adds culturally-significant species to restoration targets and traditional management practices to achieve ecological resilience. We compare 11 attributes of WEK and TEK that aid ecological restoration; all are complementary or shared by these two ways of knowing. Both WEK and TEK emphasize adaptive approaches for managing natural resources, as mandated in the Delta Plan. We suggest that WEK–TEK restoration sites throughout the Delta can be linked (virtually) to honor cultural integrity and nurture a “Sense of Place” for Native Californians and others. At the same time, such a network could foster ways to achieve sustainability through the TEK ethic of reciprocity, which WEK lacks. A network of WEK–TEK sites could enhance unique cultural values while supporting passive recreation and attracting ecotourists.

An extreme decline in Delta Smelt (Hypomesus transpacificus) abundance has led to a number of management actions to support this endangered species, including the development and refinement of culture techniques and the creation of a refuge population. The wild Delta Smelt population has diminished to the point that many in the scientific community believe population supplementation using cultured fish needs to be experimentally evaluated as a possible management tool. Concerns about supplementation include the effectiveness of this action, and its potential to divert attention and funding from other needed management actions such as habitat restoration. Here, we describe the outcomes of a 2-day workshop that described the current refuge population, and identified key issues for potential future use of cultured Delta Smelt for research and management. Expanded use of cultured Delta Smelt is controversial and requires consideration for complexities that include legal constraints and permitting requirements. Developing policies that allow for in situ experiments using cultured Delta Smelt appears to be a precursor for advancing policies that might allow supplementation actions. Releases of cultured fish, either experimentally or as a management action, clearly need to be conducted within an adaptive management program that is integrated with other strategies, including habitat restoration. We describe a general framework for evaluating the potential risks of supplementation and include suggestions for how to reduce risks and uncertainty. Overall, we conclude there is sufficient baseline information about Delta Smelt and the existing culture program to proceed with targeted field research that utilizes cultured fish. Finally, given the dire status of this species, we conclude that rapid progress toward the development of a viable and testable supplementation program must be a priority for Delta Smelt conservation.

We studied abundance and dynamics of zooplankton in the tidal freshwater Cache Slough Complex (CSC) in the northern Delta of the San Francisco Estuary during June, July, and October 2015. We asked whether the CSC was an area of high zooplankton production that could act as a source region for open waters of the estuary. Abundance of the copepod Pseudodiaptomus forbesi was similar to that in freshwater reaches of the central and eastern Delta and higher than that in the adjacent Sacramento River. Growth rate of P. forbesi was higher than previously measured in large estuarine channels because of higher temperature and phytoplankton biomass in the CSC. Samples of P. forbesi examined with molecular techniques contained an unexpectedly high proportion of DNA from cyanobacteria and little DNA from more nutritious phytoplankton. We also examined tidal exchanges of phytoplankton biomass and copepods between Liberty Island, a shallow tidal lake within the CSC, and the adjacent southern Cache Slough, which links the CSC to the Sacramento River. We calculated zero net flux of phytoplankton over 127 days between June and October. The tidal flux of copepods, calculated using tidal flow from an in situ flow station and half-hourly sampling over three 24.8-hr tidal cycles, varied a great deal because of temporal patchiness and day/night variation in abundance. Overall, the tidal flux was indistinguishable from zero, while the tidally-averaged water flow (and therefore the net copepod flux) was always into the wetland. Our results show some promise for the CSC as a productive habitat for planktivorous fishes and as a laboratory for learning how to design future wetland restoration. However, we remain cautious about whether wetlands such as the CSC may export large quantities of food organisms that can support fishes in other regions of the estuary.

Tag effect studies are paramount in interpreting the results of survival studies. The objective of this study was to analyze the influence of tag implantation and tag burden on the survival, tag retention, growth, and wound healing of juvenile Chinook Salmon 7.8 ± 0.9 g initial weight. Fish were obtained from the Merced River Hatchery, held for 7 d, and then surgically implanted with Juvenile Salmon Acoustic Telemetry System (JSATS) SS300 dummy tags (0.3 g in air). Tag burden ranged from 2.9–4.8% (3.86 ± 0.43%, mean ± standard deviation). Weight and fork length were taken immediately before tag implantation. All fish (i.e., control and dummy-tagged) were also implanted with a visible implant alpha tag next to the dorsal insertion. Control and dummy-tagged fish were held in a single tank for 30 d. Any fish that died during the 30-d period were noted. At the end of the holding period, all fish were euthanized, weighed, measured, and necropsied. All dummy-tagged fish retained their dummy tag, and survival rates between the two groups were similar. Wound healing was also similar across the range of tag burdens analyzed. Specific growth rates, however, differed significantly between the two groups, with control fish growing at a rate of 1.08 ± 0.38% d^{− 1} compared to 0.55 ± 0.48 % d^{− 1} in dummy-tagged fish (P < 0.001). Tag burdens and specific growth rates for dummy-tagged fish (P = 0.961) did not correlate, nor did initial weight and specific growth rate for control (P = 0.363) or dummy-tagged (P = 0.983) fish. The cause of the decreased growth rate in dummy-tagged fish remains unknown. Determining the cause of decreased growth in tagged juvenile Chinook Salmon, and how that decreased growth may influence survival in the wild, should be investigated further.

The San Francisco Estuary and its upstream watershed have been highly altered by human development following the California Gold Rush in the mid-19th century. In this paper, we explore the inter- and intra-annual variability of freshwater flow to this estuary and the resulting salt intrusion under scenarios that represent pre-development and contemporary conditions. To place this comparison in context with the advent of systematic and accurate flow and salinity measurements in the estuary, we consider an additional “pre-project” scenario that represents early 20th-century water management (circa 1920), after major flood control and reclamation but before the introduction of large water storage, diversion, and export operations. We use an observed climate record that spans 82 years to compare freshwater flow associated with the scenarios’ landscape and water use characteristics. Using published relationships between flow and salt intrusion length developed from three-dimensional hydrodynamic modeling, we evaluate the effect of these flow alterations as well as estuarine geometry modifications and historically-observed sea-level rise on salt intrusion. We conclude that the pre-development estuary exhibited a more seasonally-variable salinity regime, resulting from a more variable inflow regime from the upstream watershed.

Many western U.S. landscapes are managed for multiple objectives, including biological conservation, commodity production, human welfare, and recreation. Effective conservation of special-status species in managed landscapes is challenging when species protection must be balanced with broader land-management objectives. In managed river systems, actions such as channel maintenance, bank stabilization, dam operation, and habitat enhancement are often implemented to achieve objectives related to water delivery, flood control, protection of adjacent lands, public recreation, and biological conservation. However, these actions are often constrained by the presence of special-status species because of regulatory requirements that may supersede implementation of other measures. Strategies to balance special-status species conservation with broader management objectives are directly informed by robust data sets on species abundance and distribution. On lower Cache Creek in Yolo County, California, multi-objective management seeks to balance protection of the federally-threatened Valley elderberry longhorn beetle (Desmocerus californicus dimorphus) and its sole host shrub, blue elderberry (Sambucus nigra ssp. caerulea), with channel maintenance, bank stabilization, and habitat enhancement actions. We conducted a comprehensive field survey from 2015 to 2016 to map all elderberry shrubs across the 904-ha Cache Creek Resource Management Plan area. An estimated 10,296 shrubs that spanned small, medium, and large size classes were mapped, strongly suggesting that the local population has been increasing since in-channel mining ceased in 1996. Analyses of shrub distribution relative to floodplain inundation zones, and associated vegetation, slope, and aspect revealed that most shrubs occurred in association with other woody riparian vegetation and within the ≤ 10-yr floodplain inundation zone. In addition, shrubs occurred more often than expected on intermediate slopes and both westerly and northwesterly aspects. The results of this study are guiding adaptive management and informing project planning and permitting on lower Cache Creek, demonstrating the importance of spatially-explicit abundance and distribution data for special-status species in managed landscapes.