Desert ecosystems are particularly susceptible to anthropogenic influences. This is especially true for desert aquatic systems where limited water resources can be easily impaired by excessive water mining depleting the underlying aquifers. Although the aquatic environments and their associated native fishes are declining throughout the Chihuahuan Desert, we will focus on examples from the Big Bend region, the Balmorhea Springs Complex, the Pecos River region, and the Devils River region. Ongoing and impending land use and water consumption patterns suggest even further reductions in the near future. Even though numerous conservation activities are underway, archaic Texas water laws must be revisited and reformulated if the desert aquatic systems are to be truly conserved for more than the immediate future.