San Francisco Estuary and Watershed Science

Science is the foundation for a wide range of activities, including evaluation, innovation, and technology, which in turn support management. Without good science, resource management in regions such as the San Francisco Estuary is handicapped, and must proceed with outdated conceptual models, operating strategies, and technologies. At the same time, we recognize that poor communication can interfere with conversations between scientists and managers, even when high-quality data and publications are available. In this essay, we have tried to address an important part of this issue: helping scientists to understand how to produce actionable science. Our hope is that these suggestions will, at the least, help improve dialog between scientists and the managers responsible for the estuary’s resources.

Subsets of annual and sub-annual tree-ring chronologies are used to reconstruct seasonal precipitation totals in northern California. The specific seasons selected for reconstruction are based on the strongest monthly precipitation signals recorded in the tree-ring data. Earlywood width of gray pine is best correlated with Oct-Dec precipitation at the onset of the wet season. Latewood width of ponderosa pine is correlated with Mar–Apr totals at the end of the wet season. These earlywood and latewood width chronologies are used to develop separate reconstructions of precipitation for the “autumn” (Oct–Dec) and “spring” (Mar–Apr) seasons. Total ring-width chronologies of blue oak are highly correlated with October–April precipitation totals and are used to reconstruct precipitation for the “wet season.” We then computed one additional skillful reconstruction by subtracting the reconstructed spring totals from the wet season precipitation estimates (i.e., “winter” [Oct–Feb]). We compare the winter and spring reconstructions because they are well calibrated and provide an interesting long-term perspective on the interaction of winter–spring precipitation amounts near March 1, when important reservoir management decisions are often made. Consecutive wet winter and very wet spring precipitation anomalies increased after 1950 in the instrumental and reconstructed time-series, often coinciding with the largest spring streamflow and flood events recorded on the American River at Folsom. Once the sub-annual tree-ring data can be improved, it may be possible to develop discrete reconstructions of early-, middle-, and late-season precipitation for the past 250 to 500 years, to help define natural variability and anthropogenic forcing of seasonal precipitation totals in California.

Phytoplankton subsidies from river inputs and wetland habitats can be important food sources for pelagic organisms in the Sacramento–San Joaquin Delta (Delta). However, while the Sacramento River is a key contributor of water to the Delta, providing 80% of the mean annual inflow, the river is only a minor source of phytoplankton to the system. The reason for low phytoplankton biomass in the Sacramento River is not well understood but appears to be associated with a 65-km stretch of the lower river where chlorophyll-a (Chl-a) concentrations can decline by as much as 90%. We conducted two surveys along the lower Sacramento River, in spring and fall of 2016, to investigate the relative contributions of different factors potentially driving this Chl-a decline. Our study evaluated the change in Chl-a concentrations as a result of dilution from tributaries, light availability, nutrient concentrations, nutrient uptake, phytoplankton productivity, zooplankton grazing, and clam grazing. Chl-a concentration decreased from 14 µg/L to 1.8 µg/L in the spring and from 4.0 µg/L to 1.2 µg/L in the fall. Dilutions from the Feather River and American River contributed 39% and 11% of Chl-a declines, respectively, during the spring. Average water depths roughly doubled downstream of the American River confluence, reducing water column light availability and lowering productivity. Zooplankton and clam grazing rates were generally low. Using a mass balance analysis, the measured variables explained 76% of the observed decline in Chl-a in the spring, suggesting additional losses from unidentified factors. We found that phytoplankton biomass is regulated by multiple potential factors in the lower Sacramento River, emphasizing the need for practitioners of restoration and management programs to evaluate multiple potential loss factors when attempting to enhance phytoplankton production in the Delta, or other large river systems.

We investigated wind-wave and suspended-sediment dynamics in Little Holland Tract and Liberty Island, two subsided former agricultural tracts in the Cache Slough complex in the northern Sacramento-San Joaquin Delta which were restored to tidal shallows to improve habitat. Turbidity, and thus suspended-sediment concentration (SSC), is important to habitat quality because some species of native fishes, including the Delta Smelt, are found preferentially in more turbid waters. Data from October 2015 to August 2016 show that average SSC was greater within Little Holland Tract than in the primary breach that connects the basin to surrounding channels: approximately twice as great at a shallower station farther from the breach and 15% greater at a deeper station closer to the breach. Suspended-sediment concentration within Little Holland Tract was directly related to wave shear stress and inversely related to water depth, based on linear regression. We used measurements of suspended-sediment flux (SSF) through the largest levee breaches to assess whether the enhanced SSC within Little Holland Tract is exported to surrounding waters, thus potentially increasing turbidity over a wider region. Cumulatively, sediment is exported through the Little Holland Tract breaches in winter and imported in summer, consistent with regional patterns in sediment flux, indicating that wind-wave re-suspension within the basin does not control sediment flux from Little Holland Tract on seasonal time-scales. Some sediment was exported during wind-wave events, and results show that sediment export is greater when primary breaches are located downwind of the basin rather than upwind.