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With increasing global scarcity of freshwater, groundwater aquifers are an increasingly valuable reserve. However, anthropogenic activities endanger integrity of groundwater resources through excessive withdrawal, insufficient recharge due to landscape changes, and contamination with foreign substances. Bioremediation to degrade contaminants in situ using native or augmented microbial communities is an increasingly popular strategy. While bioremediation is frequently economically favorable, the mechanisms and agents of compound degradation and long term ecological consequences are scarcely comprehended. This thesis is an investigation of microbial community structure and dynamics during a bioremediation event to attenuate an aquifer plume of the explosive compound RDX (Hexahydo-1,3,5-Trinitro-1,3,5-Triazine) originating from the Iowa Army Ammunition Plant in southeast Iowa. Structure and dynamics of the native and altered aquifer microbial community was examined using culture-independent DNA based profiling methods in addition to state of the art high throughput sequencing of whole community rRNA genes. A variety of statistical approaches were used to resolve temporal and spatial sample relationships and novel organisms were differentiated from known taxa using phylogenetic constructions from DNA sequences I collected. Interrogation of the Bacterial community dynamics during the bioremediation revealed a unique Geobacteraceae dominated community coincident with RDX degradation and metabolite accumulation. Census of the 18s rRNA gene sequences collected from deep sediment cores and wells exposed a surprisingly diverse subsurface eukaryotic community dominated by previously unobserved groups within the Fungi and Platyhelminthes (flatworms) Finally, a unique group of the recently discovered group known as the cryptomycota was present in the aquifer. Comparison to sequences from marine and surface freshwater high throughput sequence sets provides evidence that one prominent group of aquifer cryptomycota may have originated from marine ancestors. his work yielded two primary innovations. The first was providing the first evidence linking RDX degradation to specific microorganism at the field scale. The second and most significant contribution was the revelation and characterization of a subsurface eukaryotic community. Current groundwater management practices fail to account for these ecosystem participants who likely contribute to predation, nutrient recycling, and possible contaminant degradation