Conflicts related to groundwater and aquifers are peculiar. Groundwater is inconvenient to water law and water diplomacy because it is hidden and referenced differently than surface water. The groundwater container, the aquifer storing groundwater, is part and parcel of the groundwater debate, but rarely is discussed at the same table of surface water and groundwater. Part of the problem focuses on the value of groundwater by scientists and engineers trained in the tradition of multiple working hypotheses. Tension exists between technical training and traditional knowledge of groundwater through local stories and myths. Boundaries used to develop and manage groundwater and aquifers are conflictive because of the lack of standard methodologies, as well as the social and technical differences in developing hydrogeologic conceptual models. As the subsurface is increasingly relied upon for changing conditions for energy, waste, and water management, pracademics in water negotiations need to integrate multiple frameworks and transdisciplinary skills-building situations to enhance cooperation over groundwater and aquifers.