The natural complexity, heterogeneity, and extent of transboundary aquifers around the world, have led to controversy over which method or criteria should be used to identify and delineate their boundaries. Currently, there is no standard methodology that aquifer-sharing countries can use to delineate the area of a transboundary aquifer. In the case of Mexico and Texas, Mexico uses administrative boundaries, whereas Texas uses geological boundaries. This paper proposes a method for delineation and prioritization of aquifers (or aquifer areas) called effective transboundary aquifer areas (ETAAs), which uses a combination of physical criteria (geological boundaries, topography, and hydrography) and the location and density of active water wells in the borderland between Mexico and Texas. This method identifies the area of priority (productivity area) in the aquifer using pumping patterns or hot spots regardless of the aquifer’s surficial geological limits, therefore offering a more effective, local and practical management option at the transboundary level. Different geological features or pumping patterns will have different sizes and locations of ETAAs within the same aquifer. In West Texas, which is dominated by bolsons, the method produces limited options for ETAAs, whereas in South Texas in the easternmost border the identified ETAAs are more significant.