San Francisco Estuary and Watershed Science

Significant wetland losses and continuing threats to remnant habitats have motivated extensive restoration efforts in the San Francisco Bay–Delta estuary of California, the largest in the western United States. Consistent monitoring of ecological outcomes from this restoration effort would help managers learn from past projects to improve the design of future endeavors. However, budget constraints and challenging field conditions can limit the scope of current monitoring programs. Geospatial tools and remote sensing data sets could help complement field efforts for a low-cost, longer, and broader monitoring of wetland resources. To understand where geospatial tools could best complement current field monitoring practices, we reviewed the metrics and monitoring methods used by 42 wetland restoration projects implemented in the estuary. Monitoring strategies within our sample of monitoring plans relied predominantly on field surveys to assess key aspects of vegetation recovery while geospatial data sets were used sparingly. Drawing on recent publications that focus on the estuary and other wetland systems, we propose additional geospatial applications to help monitor the progress made toward site-specific and regional goals. These include the use of ecological niche models to target on-the-ground monitoring efforts, the up-scaling of field measurements into regional estimates using remote sensing data, and the analysis of time-series to detect ecosystem shifts. We discuss challenges and limitations to the broad-scale application of remote sensing data in wetland monitoring. These notably include the need to find a venue to store and share computationally intensive data sets, the often cumbersome pre-processing effort needed for long-term analyses, and multiple confounding factors that can obscure the signal of remote sensing data sets.

Water budgets integrate and summarize the water inputs and outputs that are essential for effective water resources management. Using water data collected from different sources, we constructed three water budgets (a 12-year annual average, a wet year, and a critically dry year) for the Sacramento–San Joaquin Delta (Delta), the Sacramento River (SR) watershed, and the San Joaquin River (SJR) watershed. Although multiple water budgets for the Delta exist, the water budgets presented here are the first to provide all three of the following: (1) water budgets for the entire Delta watershed, divided into management-relevant components, (2) comparisons between wet and dry years and between different regions of the watershed, and (3) discussion of major gaps and uncertainties in the available water data to guide and inform future data collection and water management. Results show that, from 1998 to 2009, the Delta received 24.2 million acre feet (maf) of water each year on average, which primarily exited the Delta as river outflow (71%), water exports (22%), and evapotranspiration (ET; 6%). The SR watershed received 56.9 maf of water (95% as precipitation). The major outputs from the SR watershed were ET (63%) and flows to the Delta (34%). In the SJR watershed, total water input was 28.7 maf composed of precipitation (74%), water imported from the Delta (18%), and storage depletion (7%). The major outputs from the SJR watershed were ET (65%), water exports (19%), and flows to the Delta (14%). Most values varied greatly from year to year. Although streamflows, water exports, and valley precipitation are relatively well measured and estimated, uncertainties are higher for groundwater storage change as well as for ET and precipitation in montane regions. Improvement in data collection and synthesis in these components is necessary to build a more detailed and accurate water budget.

We evaluated two historically important data sets to characterize the San Francisco Estuary’s salinity regime before the State of California began systematic data collection in the early 1920s. One set documents barge travel along the Sacramento and San Joaquin rivers to obtain water of adequate quality for local industry; a second set documents Delta inflow used to compute antecedent outflow. The barge travel distance reported over 2 decades (1908–1929) was well explained by flow–salinity modeling, indicating internal consistency in these measurements. However, absolute salinity intrusion estimated through the barge travel data is systematically lower than suggested by contemporaneous water-quality measurements available since 1921. Through integration of these data sets, our work showed substantial similarities between 1908–1921 and the subsequent period before construction of Shasta Dam (1922–1944). Our analysis reveals an apparent shift in the estuary’s salinity regime, with lesser salinity intrusion occurring in pre-1919 summer and fall months as a result of higher summer Delta outflow; this shift may be related to lower storage and irrigation diversions as well as a preponderance of wet years with higher summer runoff in the pre–1919 period. We found seasonal patterns of wet year salinity intrusion to be comparable over the full study period (1908–1944), indicating that the relative effect of upstream water management is minimal when flows are high, consistent with findings reported in later periods. The barge and flow data provide qualitative insights on early 20th century conditions, when limited data are available. Post–1920 hydrology and salinity data are preferable for quantitative analyses because of better documentation associated with collection and analysis, and sustained reporting over several decades. This work provides a foundation for future efforts to characterize the hydrologic and hydrodynamic changes that occurred in the system between the 1850s (i.e., natural or pre-development conditions) and the 1920s.

Invasive species have many detrimental ecological and socio-economic effects. However, invasive species can also provide novel habitat for native species. The growing rate of biological invasions world-wide presents an urgent dilemma: how can natural resource managers minimize negative effects of invasive species without depleting native taxa that have come to rely on them? Adaptive management can provide a means to address this dilemma when invasive species management plans are crafted in novel environments. We present a case study of research in support of adaptive management that considers the role of invasive water hyacinth (Eichhornia crassipes [Mart.] Solms [Pontederiaceae]) management, using herbicides, in aquatic food web functioning in the Sacramento–San Joaquin River Delta of California, USA (the “Delta”). We hypothesized that herbicide applications under current management protocols would reduce the abundance and diversity of aquatic invertebrates because they would alter both structural and biological habitat. Using a Before, After, Control, Intervention (BACI) experiment, we sampled invertebrates per gram plant biomass before and 4 weeks after glyphosate applications in treated and untreated locations. There was more plant biomass in the late-season samples because dead, dying, and living plant materials were compacted. However, there were no detectable differences between control and treated sites — or for samples before versus after the treatment date—for invertebrate abundance, species richness, or evenness. This case study demonstrates that even decaying water hyacinth serves as habitat for invertebrates that may be forage for Delta fishes. We concluded that current management practices using glyphosate do not affect invertebrate abundance during a month-long period of weed decay. These results provide valuable feedback for the “evaluate and respond” component of the adaptive management process for water hyacinth control, and demonstrate how managers globally can and should consider potential food web effects in the course of their invasive species management efforts.