The Fish Creek–Vallecito basin contains a 5.5-km-thick section of late Miocene to early Pleistocene sedimentary rocks exposed in the hanging wall of the West Salton detachment fault. These deposits preserve a high-fidelity record of late Cenozoic subsidence and basin filling that resulted from deformation in the San Andreas fault system of southern California. Existing and new paleomagnetic data, combined with new U-Pb zircon ages of two tuffs high in the section, show that the section ranges in age from ca. 8.0 ± 0.4 Ma at the base to ca. 0.95 Ma at the top. Geohistory analysis reveals: (1) moderate subsidence (0.46 mm/yr) from ca. 8.0 to 4.5 Ma; (2) rapid subsidence (2.1 mm/yr) from 4.5 to 3.1 Ma; (3) moderate subsidence (0.40 mm/yr) from 3.1 to 0.95 Ma; and (4) rapid uplift and erosion that has exhumed the section since ca. 1 Ma. Onset of sedimentation at ca. 8.0 ± 0.4 Ma records earliest extension or transtension in the area, possibly related to localization of the Pacific–North America plate boundary in the Salton Trough and Gulf of California. Alternatively, marine incursion at 6.3 Ma may be the earliest record of plate-boundary deformation in the Gulf of California–Salton Trough region. A thick interval higher in the section records progradation of the Colorado River delta into and across the basin starting ca. 4.9 Ma. Progradation continued during an abrupt increase in subsidence rate at 4.5 Ma, and fluvial-deltaic conditions persisted for 1.4 m.y. during the rapid-subsidence phase, indicating that delta progradation was driven by a large increase in rate of sediment input from the Colorado River. Uplift and inversion of the basin starting ca. 1.0 Ma record initiation of strike-slip faults that define the modern phase of dextral wrench tectonics in the western Salton Trough.