Habitat fragmentation is a global environmental challenge, and the marshes of southeastern Louisiana are a hotspot for habitat fragmentation. Evaluating marsh ecosystems during the transition from intact to fragmented is critical to predict future changes and inform effective conservation and restoration plans. We sampled three sites in Terrebonne Basin, Louisiana to characterize a fragmenting emergent-vegetation dominated system, investigate the relationship between plant species richness and diversity and marsh fragmentation, and determine the relationship between marsh fragmentation and cover of submerged aquatic vegetation (SAV). Emergent plant richness and diversity were higher in areas with low salinity and high surface elevation. Although these areas had relatively low fragmentation, there was no direct relationship between richness or diversity and measures of marsh fragmentation. Despite greater light availability in highly fragmented areas, SAV was restricted to areas with low fragmentation, suggesting light availability was not the factor limiting SAV colonization into open water areas. Results from this study highlight the complex interactions of geomorphological and biotic processes within a fragmenting marsh and suggest that physical drivers such as salinity and elevation are a better indicator of emergent plant community structure in this system than degree of fragmentation.