Soils, and the microbial communities contained within them, are vital for most chemical, physical, and biological processes. This study investigated how microbial community structure responded to environmental changes, such as hydrology, across vertical space (depth) and time in an emergent fresh water wetland. Research was conducted in a non-tidal freshwater wetland along the James River (Charles City County, Virginia) by establishing plots in two areas that experienced different hydrologic regimes and plant communities. Soil cores (30 cm) were collected monthly from January 2008 to February 2009, and then every two to three months thereafter until October 2009, for a total of 17 sampling events. The soil cores were divided by depth (Top: 0 – 10 cm, Bottom: 20 – 30 cm) and analyzed for a variety of soil properties including: pH, organic matter (OM), water content (WC), C:N, redox, and root biomass. Additionally, above-ground plant communities were monitored during the growing seasons. Based on preliminary analysis, one date from each season (Winter, Spring, Summer, and Fall) from both sampling years were selected for in depth analysis of the microbial community structure via Terminal Restriction Fragment Length Polymorphism (T-RFLP) of 16S-rRNA. Analysis of variance (ANOVA) found significant differences were found between the environmental parameters in regards to site, depth, and season. Three physical-chemical variables (WC, OM, and redox) were different between sites, but the majority of environmental parameters were significantly different between depths and seasons. The dominant environmental effect on microbial communities was soil depth and, overall, no seasonal patterns were observed in the microbial communities. Further, archaeal communities were most strongly correlated to changes in water content, while redox was strongly correlated to changes across depth in the bacterial communities. Collectively, these results demonstrate that wetland microbial communities are not a product of one separate variable or spatial scale, but result from various factors interlinked to shape microbial communities. More long-term studies are needed to investigate interactions between microbial community structure and environmental variables in these dynamic ecosystems.