The Sacramento–San Joaquin Delta (Delta) in California (USA) is an important part of the state’s freshwater system and is also a major source of agricultural and natural resources. However, the Delta is traversed by a series of faults that make up the easternmost part of the San Andreas fault system at this latitude and pose seismic hazard to this region. In this study, we use new high-resolution chirp subbottom data to map and characterize the shallow expression of the Kirby Hills fault, where it has been mapped to cross the Sacramento River at the western extent of the Delta. The fault is buried here, but we document a broad zone of deformation associated with the eastern strand of the fault that changes in character, along strike, across ~600 m of the river channel. Radiocarbon dates from sediment cores collected in the Sacramento River provide some minimum constraints on the age of deformation. We do not observe evidence of the western strand as previously mapped. We also discuss difficulties of conducting a paleoseismologic study in a fluvial environment.