Headwater wetland streams comprise a significant proportion of aquatic habitats in the Southeast. Nonetheless, little is known about their fish communities. I examined seasonal fish community structure and habitat use in headwater wetland and confined channel streams during 2003-2004. Species richness and fish density were greater in wetland streams than in confined channel streams. Wetland fish communities, however, varied seasonally. Species richness and fish density in wetlands were positively related to dissolved oxygen concentrations, which were strongly influenced by stream discharge. During the winter, species richness and total fish density were positively related to stream temperature and negatively to current velocity, with the former influenced by groundwater inputs. Findings from this study suggest that wetland headwater streams were important stream fish habitats. The greater sensitivity of wetland stream habitats to low flows also suggests that streamflow regulations developed in confined channel streams may not be adequate for wetland headwater streams.