Human-induced and natural processes continue to act upon the estuaries of the northern Gulf of Mexico. Predictive models have been applied to project the interactions between habitat modification and population estimates for some estuarine species. However, these assessments may be furthered by focusing on a suite of species, such as a subset of the marsh birds that inhabit these ecosystems. During 2004 and 2005, we conducted point count surveys within the estuarine systems of Alabama and Mississippi, USA to assess whether small-scale wetland characteristics and a broader scale metric of habitat modification influenced the distributions of several marsh bird species: clapper rail (Rallus longirostris), common yellowthroat (Geothlypis trichas), least bittern (Ixobrychus exilis), marsh wren (Cistothorus palustris), and seaside sparrow (Ammodramus maritimus). On the basis of current habitat, we project change in species occupancy through several scenarios. Projections suggest that habitat alteration through loss of emergent marsh and increased cover of the halophyte Juncus roemerianus may be most influential to the distribution of these marsh bird species. Thus, continued alteration of existing conditions coupled with sea-level rise will likely have a significant impact on the distribution of this group of marsh bird species as well as the integrity of their habitat.