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Wetland restoration is a key management tool for increasing food availability for at-risk fishes in the San Francisco Estuary. To characterize the benefits of restoration sites, it is critical to quantify the abundance and composition of fish food resources in and near the wetlands. Characterization of zooplankton communities is considered particularly important, but accurate analysis of zooplankton samples is time-consuming and expensive. The recently established Fish Restoration Program (FRP) Monitoring Team assessed whether data from existing long-term monitoring surveys could be used to characterize shallow-water zooplankton communities prior to restoration. During the springs of 2017-2019, FRP collected zooplankton samples near the mouth of tidal wetland sites, or immediately outside future restoration sites, and compared them to concurrent samples collected in deep water by existing long-term monitoring surveys. We found very few differences in community composition between shallow and deep samples, though a few taxa were more abundant in shallow water. Seasonal and inter-annual differences in composition and abundance showed that restoration sites provide varying food resources over time. There was significantly higher total abundance of zooplankton in deep versus shallow water, which may be due to differences in zooplankton production, migration, or fish predation. There may also be inconsistencies in towing speed and gear type driving this result, rather than true habitat differences. This study indicates that monitoring of wetland restoration sites must rely on multiple years of data collected on the site, rather than relying on adjacent open-water sampling, and should include monitoring of epiphytic and epibenthic invertebrates as well as zooplankton.