Comparison of the relative abundance of fish species from different life-history groups and their temporal patterns of estuarine habitat use from two estuaries north and south of Cape Cod indicates that the Cape acts as a zoogeographic boundary. Between April 1988 and December 1989, monthly seine and trawl samples were collected from nearshore, shallow-water marsh, and beach and deeper open-water habitats in Wells Harbor, Maine, and Waquoit Bay, Massachusetts. Forty-eight species and 80,341 individuals were collected from Waquoit Bay compared to 24 species and 22,561 individuals from Wells Harbor. Waquoit Bay had proportionally fewer resident species and more marine, nursery, and occasional species than Wells Harbor. Annual density and biomass values were greater across all habitats in Waquoit Bay, with the summer values from the marsh habitat an order of magnitude higher than comparable summer data from the Wells habitats. We suggest that marsh and beach habitats provide a nursery area for young-of-the-year fishes, while deeper, open-water habitats serve as a corridor for fishes moving to nearshore habitats or serve as a refuge during low tide.