The Salton Trough represents a complex transition between the spreading center in Baja California and the strike-slip San Andreas fault system and is one of the most active zones of deformation and seismicity in California. We present a high-resolution interseismic velocity field for the Salton Trough derived from 74 continuous GPS sites and 109 benchmarks surveyed in three GPS campaigns during 2008–2009 and previous surveys between 2000 and 2005. We also investigate small-scale deformation by removing the regional velocity field predicted by an elastic block model for Southern California from the observed velocities. We find a total extension rate of 11 mm/yr from the Mesquite Basin to the southern edge of the San Andreas Fault, coupled with 15 mm/yr of left-lateral shear, the majority of which is concentrated in the southern Salton Sea and Obsidian Buttes and is equivalent to 17 mm/yr oriented in the direction of the San Andreas Fault. Differential shear strain is exclusively localized in the Brawley Seismic Zone, and dilatation rate indicates widespread extension throughout the zone. In addition, we infer clockwise rotation of 10°/Ma, consistent with northwestward propagation of the Brawley Seismic Zone over geologic time.