In Mexico, the evaluations of environmental flows are regulated by the Mexican Norm NMX-AA-159-SCFI-2012 and they warrant the establishment of water reserves for the environment. Yet, the pressure for water use limits the establishment of said reserves. This research aimed to evaluate the changes through time of the variables that serve as a basis for the implementation strategy by the Mexican government. A geographical information system was built with updated variables, the desired conservation status was analyzed, and the potential reserves were estimated based on the reference values for all basins nationwide. The results were examined according to their historical, current, and potential contribution to the conservation of natural protected areas and their connectivity. The outcomes point towards an administrative implementation strategy with positive outcomes despite the growing pressure for water use, with a change rate higher than the one for the creation of new protected areas. Currently, basins with low pressure and high conservation value have the potential to contribute to 86–88% of the goal set by the present administration without affecting water availability. Finally, reserving water in the priority basins would guarantee the legal protection of the flow regime in 48–50% of the hydrographic network in a desired conservation status, 45–49% of wetlands of international importance, and other natural protected areas in 85–89% of the global ecoregions represented in Mexico.