Stratigraphic evidence for coseismic subsidence has been documented in active-margin estuaries throughout the world. Most of these studies have been conducted in subduction zone or strike-slip settings; however, the stratigraphic response to coseismic subsidence in other tectonic settings would benefit from further study. Here we show evidence of late Holocene coseismic subsidence in a structural estuary in southern California. Below the modern marsh surface, an organic-rich mud containing marsh gastropods, foraminifera, and geochemical signatures indicative of terrestrial influence (mud facies) is sharply overlain by a blue-gray sand containing intertidal and subtidal bivalves and geochemical signatures of marine influence (gray sand facies). We use well-established criteria to interpret this contact as representing an abrupt 1.3 ± 1.1 m rise in relative sea level (RSL) generated by coseismic subsidence with some contribution from sediment compaction and/or erosion. The contact dates to 1.0 ± 0.3 ka and is the only event indicative of rapid RSL rise in the 7 k.y. sedimentary record studied. Consistent with observations made in previous coseismic subsidence studies, an acceleration in tidal-flat sedimentation followed this abrupt increase in accommodation; however, the recovery of the estuary to its pre-subsidence elevations was spatially variable and required 500–900 years, which is longer than the recovery time estimated for estuaries with larger tidal ranges and wetter climates.