The ENIGMA project seeks to discover, characterize the reciprocal interactions between the microbial communities and the geochemical and geophysical parameters of the shallow subsurface within the contamination plume of groundwater and sediment microbiomes in the shallow subsurface at the contaminated Oak Ridge Field Research Site (FRC). Our ambition is to do so at sufficient resolution to causally predict the active biotic and abiotic mechanisms mediating key processes such as denitrification; dissect the dispersing and persistent microbial community components critical in space and time during these processes, and ultimately predict the future changes in contaminant fate from current observations and possibly arising from natural and anthropogenic perturbations. Outcomes are significant both in the basic science of community ecology and in gaining an applied understanding of biologically-mediated subsurface processes in contaminated sediments. The FRC contains highly contaminated DOE legacy regions and excellent field infrastructure available for research instrumentation and 30+ years of biogeochemical data collected by other scientists. It has well-mapped hydrology and geology and complex gradients of nutrients, stressors, and contaminants, making the FRC an excellent site to study the reciprocal interactions of environmental factors on microbial ecology and activity. Across the site, a large number of active wells permit efficient groundwater sampling, and it is relatively cost-effective to drill new wells or retrieve depth-indexed sediment cores when the project requires it.