Transitional wetlands occur along an estuarine salinity continuum bracketed by salt and nontidal freshwater wetlands. Long-term disturbances, such as sea level rise, may shift physical characteristics and hydrologic features of estuarine systems leading to transitional wetland habitat alterations, with unknown affects to associated biological communities. To begin to assess the ecological significance of a change in transitional wetland character, physicochemical parameters, and fish and invertebrate communities were surveyed seasonally in two extensive meso-oligohaline marshes, currently undergoing changes due to sea level rise. Faunal communities were similar between marshes, and included economically important species and forage fish. Temporal shifts in communities occurred seasonally and annually with high variability in species abundance among years. Drastic annual variability in salinity regimes due to extremes in precipitation occurred during the survey period driving shifts in biotic community composition.