Marsh flooding and drying may be key factors affecting seasonal nekton distribution and density because habitat connectivity and water depth can impact nekton accessibility to the marsh surface. Recent studies have characterized freshwater nekton assemblages in marsh ponds; however, a paucity of information exists on the nekton assemblages in freshwater emergent marshes. The principal objectives of this study are to characterize the seasonal nekton assemblage in a freshwater emergent marsh and compare nekton species composition, density, and biomass to that of freshwater marsh ponds. We hypothesize that 1) freshwater emergent marsh has lower taxa richness than freshwater marsh ponds; and 2) freshwater emergent marsh has a lower seasonal density and biomass than freshwater marsh ponds. Mosquitofish Gambusia affinis and least killifish Heterandria formosa were abundant species in both habitats while some abundant species (e.g., banded pygmy sunfish Elassoma zonatum) in freshwater ponds were absent in freshwater emergent marsh. Our data did not support our first and second hypotheses because taxa richness, seasonal density and biomass between freshwater emergent marsh and ponds did not statistically differ. However, freshwater emergent marsh was dry during the summer months and thus supports no fish species during this period. Additional long-term research on the effects of flow regime in the freshwater marsh on nekton assemblages would potentially improve our understanding of nekton habitat requirements.