Combined geological and geophysical investigations are used to characterize intra-basin and basin-bounding faults, constrain basin geometry, study fault interactions, and ultimately to identify areas favorable to hydrothermal flow in the geothermal system in Surprise Valley, California. We utilize high-resolution gravity and ground-magnetometer data collected along several detailed transects within Surprise Valley to identify intra-basin structures. Our data show two types of structures whose magnetic signatures differ markedly: N-S-trending normal faults and NW-SE-trending fracture zones that accommodate little offset. The geothermal system is concentrated at the intersections of these two contrasting structural trends, implying that the fracture system facilitating hydrothermal flow to hot springs in Surprise Valley is more complex than typically envisioned for Basin and Range extensional geothermal systems. Our results suggest that there are potentially many pathways for fluid flow, offering new targets for geothermal exploration.