The transboundary nature of water dividing Mexico and the United States (U.S.) transforms the entire border region into an instrument of cooperation, a source of conflict, a national security issue, and an environmental concern. Reasonable data collection and research analysis have been conducted for surface waters by joint governmental institutions and non-governmental bodies. However, with the exception of the U.S. Transboundary Assessment Act Program (TAAP) (focusing on the Hueco Bolson, Mesilla Bolson, San Pedro and Santa Cruz aquifers), there is no comparable research, institutional development, or assessment of transboundary groundwater issues on the frontier. Moreover, data collection and methodologies vary between the two countries, there is no broadly accepted definition of the transboundary nature of an aquifer, and available legal and policy frameworks are constrained by non-hydrological considerations. Hence, there is a conceptual and institutional void regarding transboundary groundwater resources between Mexico and the U.S. The purpose of this paper is to bridge this void and characterize transboundary aquifers on the Mexico–US border. It reviews existing international frameworks for identifying hydrological and social criteria that characterize an aquifer as transboundary. It then assesses data from both countries to propose where and which aquifers could be considered transboundary. Finally, the paper proposes an agenda for assessing Mexico–US transboundary aquifers as a means for improving groundwater management in the border region.