Floodplain microbial communities mediate biogeochemical transfers between terrestrial and aquatic ecosystems, and thus an investigation into the dynamics of floodplain microbial communities is necessary for an improved mechanistic understanding of biogeochemical patterns across fluvial landscapes.  Here we present microbial community data from two contrasting floodplain ecosystems: the Nyack Floodplain in northwestern Montana and the Timberlake Floodplain in coastal North Carolina.  We relate patterns in microbial community structure including diversity and similarity as assessed by terminal restriction fragment analysis (tRFLP) fingerprinting, and microbial identity through clone library sequence analysis, to changes in redox potential, electron donor and acceptor availability, and hydrology.  Additionally, we assess how temporal changes in the microbial community relate to seasonal changes in these parameters at each site.  Preliminary data indicate that bacterial community composition and abundance vary as a function of position on the floodplain, with downwelling zones generally supporting higher abundance and diversity.  Community structure information can be integrated with measures of microbial abundance and functional gene abundance to develop simulation models of carbon and nitrogen fluxes across fluvial landscapes and understand drivers of keys sites for biogeochemical transformations.