The majority of Northern California estuaries are small, flooded river valleys that are largely unstudied due to their small sizes. Yet these estuaries serve as important nursery areas for many marine fish species, including rock-fish, flatfish, smelt, and herring. In addition, they are vital to anadromous species such as Chinook Salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss). Some of these small estuaries gained protection with the completion of California's Marine Protected Area (MPA) network in 2012. From June 2014 to June 2016, we sampled the summer and winter fish communities in 3 estuaries: the Big River estuarine MPA, the Ten Mile River estuarine MPA, and the Mad River Estuary, which served as a non-MPA reference site. Fish were sampled via beach seine or fyke net at 2 stations within each estuary biannually, in summer and winter. Additional sampling was conducted in the Mad River Estuary to examine the transition from summer to winter fish communities. The fish communities in all 3 estuaries were strongly seasonal. The summer community was abundant and diverse, while winter catches were low and dominated by sculpin. Additional sampling in the Mad River Estuary showed that fish communities were diverse from spring through fall, but that catch in spring and fall was highly variable. After accounting for season, variability in the estuarine fish communities was best explained by location. The Big River Estuary had the strongest ocean connection and the most diverse marine fish community. The Ten Mile River Estuary had the weakest ocean connectivity and lowest species diversity. The Mad River Estuary fish community shared more similarities with both MPAs than they did with each other. All estuaries had a more diverse marine fish community downstream than upstream. The establishment of designated estuarine MPAs and the research presented here are important first steps to increased protection, understanding, and appreciation of the small California estuaries that cumulatively provide habitat critical to the life cycles of anadromous and marine species.