Amagmatic geothermal systems within regional-scale orogenic faults are promising renewable resources for heat and possibly electricity production. However, their behavior needs to be better understood to improve exploration and assessment of their energy potential. To provide more insight, we report a geochemical, geological, and geophysical study of seven hot spring sites strung along a 90 km segment of the Agua Blanca Fault (ABF), which traverses a mountainous region of northern Baja California, Mexico. Our results show that topographic heads drive infiltration of meteoric water deep into basement rocks, where it is heated according to the local geothermal gradient (15–24 °C/km). Our diverse dataset provides strong evidence that the flow system, magnitude, and location of the thermal anomalies are primarily controlled by the permeability of the ABF system and the hydraulic head gradients. The hot water ascends along preferentially permeable zones, discharging at temperatures from 37 °C in inland springs to 102 °C at the Pacific coast. Higher temperatures correlate positively with the degree of extensional fault displacement (a proxy for fault permeability). Correlations between hydraulic head gradients, residence times, and 3He/Hetotal of the thermal waters show that the hydraulic head gradient controls the length and depth of the flow paths. Long paths to great depths lead to long water residence times and high 3He/Hetotal fractions. Optimal conditions at the coast allow the 120 °C temperature threshold for electricity production to be reached at relatively shallow depths (< 4 km), demonstrating the potential of orogenic geothermal systems for petrothermal exploitation.