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Zooplankton are important trophic intermediaries between aquatic primary produc- ers and higher level consumers such as fish, but to date they have been little studied in intertidal marshes. This is particularly true in the San Francisco Estuary (SFE), which is heavily impacted by human activities and is being targeted for restoration of its native wetland communities. As part of a multi-year field study investigating wetland dynamics in the upper SFE, we conducted approximately quarterly sampling of the mesozooplankton (>73 µm) at 3 channels in each of 6 marshes. Here, we describe seasonal and regional variation in the composition and abundance of zooplankton, and relate these to variations in environmental conditions. Cluster analysis identi- fied 6 different marsh zooplankton communities. The 66 taxa identified included both native and non-indigenous species (NIS), with NIS being particularly dominant in the summer and autumn. Ordination analyses indicated that salinity, temperature, and other freshwater-related variables such as freshwater flow and distance to the coastal ocean were the strongest environmental driv- ers of marsh zooplankton community composition and individual abundance. Zooplankton com- munities in intertidal marshes were similar to those of open water habitats of the SFE in many regards, although differences in some taxa were observed, e.g. higher abundances of the copepod Eury temora affinis and lower abundances of tintinnid ciliates in the marshes. Apparent differ- ences in zooplankton between intertidal marsh and open water habitats, and between different regions of the estuary, could have important implications for young fish and other consumers.

Zooplankton of tidal marsh channels in relation to environmental variables in the upper San Francisco Estuary