Abstract
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.
Highlights
The San Francisco Estuary, like many coastal regions, is a heavily impacted ecosystem, with major effects from urbanization, habitat degradation, water diversions, pollution, and invasive species (Lotze 2006, 2010; Worm et al 2006)
Limitations on water diversions to protect Delta Smelt have an important role in the water supply reliability of the region, which suffers from periodic drought
In the simulation with the flow pulse removed, the model predicted a net northward transport of water through the Toe Drain past Lisbon Weir during the entire flow pulse period, with net flows only becoming southward about 45 days after the start of the flow pulse period (Figure 4A). This indicates that the flow pulse resulted in a reversal in the net flow direction through the Toe Drain past Lisbon Weir for a prolonged period of time
Summary
The San Francisco Estuary, like many coastal regions, is a heavily impacted ecosystem, with major effects from urbanization, habitat degradation, water diversions, pollution, and invasive species (Lotze 2006, 2010; Worm et al 2006). The system suffers from multiple stressors related to anthropogenic effects, including diking and draining of wetlands, water diversions, channelization, invasive species, and contaminant inputs (Cloern and Jassby 2012; Nichols et al 1986). These stressors have led to broad ecosystem changes, including a collapse of the fish communities in the upper estuary, leading to the listing of several species under the Endangered Species Act (Sommer et al 2007; Thomson et al 2010). Limitations on water diversions to protect Delta Smelt have an important role in the water supply reliability of the region, which suffers from periodic drought
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