Mathematical modeling is used in this study to assess how tectonic movement of fault blocks and fault permeability influence the present-day and paleohydrogeology of the Rio Grande Rift near Socorro, New Mexico. Our analysis focuses on active and ancient groundwater flow patterns and hot spring development within the southern La Jencia and Socorro subbasins. The best agreement between model results and present-day and paleoheat flow data was achieved by representing faults as passive surfaces and incorporating 2 km of moderately permeable (10-14.0 m2) fractured crystalline rocks into the hydrogeologic model. Quantitative results indicate that changes in groundwater flow patterns across the basin are primarily generated by the truncation/reconnection of aquifers and confining units. Calculated flow patterns help to explain the annealing of apatite fission tracks within Eocene Baca Formation clasts to the east of Socorro, potassium metasomatism mass balance constraints within Oligocene volcanics and overlying Santa Fe Group deposits, and the timing of barite/fluorite ore mineralization within the Gonzales prospect on the eastern edge of the Rio Grande Rift. We estimate that about 5% of mountain front recharge penetrates to a depth of 2.8 km below the sedimentary pile. This may have implications for water resource planners who have historically focused on groundwater resource development within the shallow alluvial deposits along the Rio Grande Rift valley.