The Mission Creek and Banning faults are two of the principal strands of the San Andreas fault zone in the northern Coachella Valley of southern California. Structural characteristics of the faults affect both regional earthquake hazards and local groundwater resources. We use seismic, gravity, and geological data to characterize the San Andreas fault zone in the vicinity of Desert Hot Springs. Seismic images of the upper 500 m of the Mission Creek fault at Desert Hot Springs show multiple fault strands distributed over a 500 m wide zone, with concentrated faulting within a central 200 m wide area of the fault zone. High-velocity (up to 5000 m/sec) rocks on the northeast side of the fault are juxtaposed against a low-velocity (<2000 m/sec) basin on the southwest side within the upper few hundred meters. Near-surface strands of the Mission Creek fault dip steeply southwestward and northeastward and merge at depth to form a narrower, steeply southwestward-dipping or near-vertical (80° to 90°) fault zone. The Banning fault, in contrast, dips northeastward (45° to 70°) toward the Mission Creek fault, and the two faults likely merge into a single San Andreas fault zone at depth, indicating a transtensional fault system. Mainshock hypocenters for two of the historically largest (M>6.0) earthquakes in the area (in 1948 and 1986) occurred at or near the depths (∼10 to 12 km) of the merged (San Andreas) fault. Large-magnitude earthquakes that nucleate at or below the merged fault will likely generate strong shaking from guided waves along both fault zones and from amplified seismic waves in the low-velocity basin between the two fault zones. The Mission Creek fault zone is a groundwater barrier with the top of the water table varying by 60 m in depth and the aquifer varying by about 50 m in thickness across a 200 m wide zone of concentrated faulting.