The present disagreements over natural gas development in the United States and abroad are currently being described as the next environmental “superdebate” – on par at least with contention over acid rain in earlier decades and at most with altercations over climate change in more recent years (Byrne, 2011). Natural gas development is controversial for a number of environmental reasons; among them, the potential harm done to groundwater systems by way of aquifer drawdown or contamination (EPA, 2011). The possibility of these harms puts society squarely in the crosshairs of the “energy-water nexus”— the tightening linkage between rising energy demand and finite water supplies, and vice versa (DOE, 2006). The energy-water nexus implies conflict in its very definition, as an intersection where the use of one resource often requires use of the other. I suggest here that groundwater systems at the energy-water nexus exacerbate one particular source of conflict, known in conflict resolution literature as a factual dispute. The concealed nature of groundwater systems make them frequent subjects of factual disputes at the energy-water nexus (Narasimhan, 2009), as demonstrated here by case studies presented at regional and local geographic scales in Colorado’s southern coalbed methane basins. At the regional scale, in the Northern San Juan Basin, a factual dispute is ongoing over whether groundwater withdrawals in the process of coal bed methane (CBM) extraction will impact overlying aquifers (Papadopulos, 2006; SJPLC, 2006; Riese et al., 2005). At the local scale, in the Raton Basin, a factual dispute is underway over a single landowner’s domestic well, which became unusable in the days following the hydraulic fracturing of a nearby CBM well for reasons that could not be determined by regulators (COGCC, 2011d). In the analysis presented here, I discuss the major uncertainties specific to groundwater systems that exacerbate factual disputes over environmental impacts. I also present ways that academic researchers might productively engage in these disputes via fact-finding efforts. I present a neutral fact-finding effort using isotopic/geochemical tracers and a groundwater monitoring guide designed to enable joint fact-finding efforts at individual domestic well sites.