Fish species composition and richness were compared among an unaltered New Jersey salt marsh and marshes altered for mosquito control, based on monthly seine collections over a year. Impounded marshes (stop-ditched and low-level impoundments) had distinctly different fish assemblages from that of an unaltered marsh. Marshes altered by open marsh water management (OMWM) techniques had tidal flows and assemblages similar to that of an unaltered marsh. The most pronounced dissimilarities in species composition were attributable to differences in salinity. Freshwater and oligohaline species dominated in low salinities, such as in some impounded areas. In the higher-salinity areas, as in OMWM and unaltered marshes, a typical estuarine assemblage was abundant. Movements of some species from OMWM and unaltered sites in winter caused characteristic changes in faunal composition and abundance. Among impoundments, however, seasonal patterns of species composition, richness, and abundance varied inconsistently. Regardless of type of alteration, salinity and habitat preference appeared to account for most of the variation in species composition and richness.