Zooplankton are a central aspect to most aquatic food webs but are often overlooked inmonitoring and restoration. California’s San Francisco Estuary (SFE), one of the most altered and invaded estuaries in North America, is one of few estuaries with a robust and long-term zooplankton sampling effort. Yet while major scientific studies have occurred in the mainstem of the estuary, backwater areas such as the Cache-Lindsey slough complex (CLC) of the north Delta have generally been neglected. These backwater areas are hotspots for zooplankton density and can often be more productive than mainstream channels. 

We present the longest time series analysis (2014-2021) of zooplankton in the CLC. Tounderstand temporal and spatial shifts in zooplankton density and its impact as a food resource, we focused on monthly springtime (March - May) zooplankton samples, when juvenile fish abundance (key planktivores) is often highest. We identify spatial zones of particularly high zooplankton density, document temporal shifts in density, and explore factors driving density changes overall. In addition to temperature and chlorophyll-α concentrations, drought conditions had a significant impact on zooplankton density. Within the CLC, the Cache network is consistently identified as an area of high zooplankton production, but there was a significant decline in zooplankton density alongside a decline in chlorophyll-α concentration.

Given the reduction of plankton and planktivorous fishes, restoration design in the regionmight consider prioritizing actions aimed at boosting fish food production. Many restoration sites in the SFE have full tidal exchange with mainstream channels, but our findings indicate how actions that increase hydraulic retention time can be beneficial. For example, constrained hydrologic connectivity, especially towards backwater locations, extends residence time and plankton production, and therefore could benefit restoration.