A pilot-scale system was established to examine the feasibility of in situ bioremediation and immobilization of U(VI) at a highly contaminated aquifer at the U. S. DOE's Field Research Center, Oak Ridge, TN. An above-ground treatment system, including a denitrifying fluidized bed reactor, was used to pre-condition the groundwater to optimize subsurface U immobilization. Ethanol to stimulate microbial reduction of soluble U(VI) to insoluble U(IV). Three monitoring wells (FW101-2, 102-2, and 102-3) were analyzed using a functional gene array containing >24,000 probes covering 10,000 genes to examine the effect of geochemistry on the functional microbial community dynamics. Microarray results indicate that, during the U (VI) reduction period, both FeRB and SRB populations reached their highest levels on day 212 in FW102-3 and on day 255 in FW102-2 and FW101-2, followed by a gradual decrease over the next 500 days in all three wells and then a rebound on day 719. Mantel tests of functional genes versus the geochemical parameters showed a significant correlation in all three wells between pH and most of the functional gene groups (p-value, <0.01-0.1) detected. The U (IV) concentrations were significantly correlated with the microbial communities in wells FW101-2 and FW102-3 over the entire study period. Once the microbial population peaked, this correlation was also observed for FW102-2, and even stronger correlations were observed in both FW101-2 and 102-3. Chemical oxygen demand (COD) correlated with the microbial community structure only in well FW101-2. Neither nitrate nor sulfate showed a significant correlation in any of the wells until after the population peak, when significant correlations were observed in FW102-2 and 102-3. Canonical correlation analysis revealed similar correlations between the functional community and the geochemical variables. In addition to correlations with the geochemical parameters, principal components analysis showed that the microbial communities also varied both temporally and spatially.