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.

While freshwater inflow has been a major focus of resource management in estuaries, including the upper San Francisco Estuary, there is a growing interest in using focused flow actions to maximize benefits for specific regions, habitats, and species. As a test of this concept, in summer 2016, we used a managed flow pulse to target an ecologically important region: a freshwater tidal slough complex (Cache Slough Complex–CSC). Our goal was to improve estuarine habitat by increasing net flows through CSC to enhance downstream transport of lower trophic-level resources, an important driver for fishes such as the endangered Delta Smelt Hypomesus transpacificus. We used regional water infrastructure to direct 18.5 million m³ of Sacramento River flow into its adjacent Yolo Bypass floodplain, where the pulse continued through CSC. Simulations using a 3-D hydrodynamic model (UnTRIM) indicated that the managed flow pulse had a large effect on the net flow of water through Yolo Bypass, and between CSC and further downstream. Multiple water quality constituents (specific conductivity, dissolved oxygen, nutrients [NO₃ + NO₂, NH₄, PO₄]) varied across the study region, and showed a strong response to the flow pulse. In addition, the lower Sacramento River had increased phytoplankton biomass and improved food quality indices (estimated from long-chain essential fatty acids) after the flow pulse. The managed flow pulse resulted in increased densities of zooplankton (copepods, cladocerans) demonstrating potential advection from upper floodplain channels into the target CSC and Sacramento River regions. This study was conducted during a single year, which may have had unique characteristics; however, we believe that our study is an instructive example of how a relatively modest change in net flows can generate measurable changes in ecologically relevant metrics, and how an adaptive management action can help inform resource management.