The Salton Trough (southeastern California, USA) is the northernmost transtensional stepover of the Gulf of California oblique-divergent plate boundary and is also where the southern terminus of the San Andreas fault occurs. Until recently, the distribution of active faults in and around the Salton Sea and their displacement histories were largely unknown. Subbottom CHIRP (compressed high-intensity radar pulse) surveys in the Salton Sea are used to develop a seismic facies model for ancient Lake Cahuilla deposits, a detailed map of submerged active faults, and reconstructed fault displacement histories during the late Holocene. We observe as many as fourteen Lake Cahuilla sequences in the Salton Sea (last ~3 k.y.) and develop a chronostratigraphic framework for the last six sequences (last ~1200 yr) by integrating CHIRP data and cone penetrometer logs with radiocarbon-dated stratigraphy at an onshore paleoseismic site. The Salton Sea contains northern and southern subbasins that appear to be separated by a tectonic hinge zone, and a subsidence signal across hinge-zone faults of 6–9 mm/yr (since ca. A.D. 940) increases toward the south to >15 mm/yr. The faults mapped to the south of the hinge zone appear to accommodate transtension within the San Andreas–Imperial fault stepover. We identify 8–15 distinct growth events across hinge-zone faults, meaning growth occurred at least once every 100 yr since Lake Cahuilla sedimentation began. Several faults offset the top of the most recent Lake Cahuilla highstand deposits, and at least two faults have offset the Salton Sea flood deposits. Active faults and folds were also mapped to a limited extent within the northern subbasin and display growth, but their kinematics and rupture histories require further study. The broad distribution of active faulting suggests that strain between the San Andreas, San Jacinto, and Imperial faults is highly distributed, thus discrepancies between geologic and geodetic slip-rate estimates from these major fault systems are to be expected.