We have studied detrital-zircon U-Pb age spectra and conglomerate clast populations from Neogene–Quaternary siliciclastic and volcaniclastic strata of the southeastern San Joaquin Basin, as well as a fault-controlled Neogene basin that formed across the southernmost Sierra Nevada; we call this basin the Walker graben. The age spectra of the detrital-zircon populations are compared to a large basement zircon age data set that is organized into age populations based on major drainage basin geometry of the southern Sierra Nevada and adjacent ranges. We find a direct sediment provenance and dispersal link for much of the Neogene between the Walker graben and the southeastern San Joaquin Basin. In early to middle Miocene time, this link was accented by the delivery of volcaniclastic materials into the southeastern Basin margin from the Cache Peak volcanic center that was nested within the Walker graben. In late middle Miocene through early Pleistocene time, this linkage was maintained by a major fluvial system that we call the Caliente River, whose lower trunk was structurally controlled by growth faults along the Edison graben, which breached the western wall of the Walker graben. The Caliente River redistributed into the southeastern San Joaquin Basin much of the ∼2 km of volcaniclastic and siliciclastic strata that filled the Walker graben. This sediment redistribution was forced by a regional topographic gradient that developed in response to uplift along the eastern Sierra escarpment system. The Caliente River built a fluvial-deltaic fan system that prograded northwestward across the lower trunk of the Kern River and thereby deflected the Kern drainage flux of sediment into the Basin edge northward. In mainly late Miocene time, turbidites generated primarily off the Caliente River delta front built the Stevens submarine fan system of the southeastern and central areas of the San Joaquin Basin. In late Quaternary time, 1–1.8 km of Caliente River–built strata were eroded as an epeirogenic uplift that we call the Kern arch emerged along the southeastern Basin margin, in response to underlying mantle lithosphere removal. The sediment that was eroded off the arch was redistributed mainly into the Maricopa and Tulare sub-basins that are located to the southwest and northwest, respectively, of the arch.