Larger nektonic fishes, many of which are economically important, comprise a large portion of the biomass in estuaries and may influence energy flow through their migrations and feeding, yet we know relatively little of this faunal component. To elucidate the patterns of species composition, distribution, and abundance in Delaware Bay, we sampled (n = 2298 sets) nektonic fishes (n = 3693 individuals, mean length = 261.4 mm, range = 53–600 mm) with multi-mesh gill nets in near-shore bay and marsh creek habitats during the summer and fall (June-November 2001) when fishes are more abundant in temperate estuaries. For the most abundant species, the older and larger individuals (age 1 ) often dominated the catches. Patterns of assemblage structure were influenced by spatial gradients in salinity and dissolved oxygen and temporal changes in temperature. Many of the large nektonic fishes that dominate in Delaware Bay are also found in other temperate estuaries from the Gulf of Maine to Chesapeake Bay, in part, because these species are highly migratory.