CHIRP seismic and swath bathymetry data acquired offshore La Jolla, California provide an unprecedented three-dimensional view of the La Jolla and Scripps submarine canyons. Shore-parallel patterns of tectonic deformation appear to control nearshore sediment thickness and distribution around the canyons. These shore-parallel patterns allow the impact of local tectonic deformation to be separated from the influence of eustatic sea-level fluctuations. Based on stratal geometry and acoustic character, we identify a prominent angular unconformity inferred to be the transgressive surface and three sedimentary sequences: an acoustically laminated estuarine unit deposited during early transgression, an infilling or “healing-phase” unit formed during the transgression, and an upper transparent unit. Beneath the transgressive surface, steeply dipping reflectors with several dip reversals record faulting and folding along the La Jolla margin. Scripps Canyon is located at the crest of an antiform, where the rocks are fractured and more susceptible to erosion. La Jolla Canyon is located along the northern strand of the Rose Canyon Fault Zone, which separates Cretaceous lithified rocks to the south from poorly cemented Eocene sands and gravels to the north. Isopach and structure contour maps of the three sedimentary units reveal how their thicknesses and spatial distributions relate to regional tectonic deformation. For example, the estuarine unit is predominantly deposited along the edges of the canyons in paleotopographic lows that may have been inlets along barrier beaches during the Holocene sea-level rise. The distribution of the infilling unit is controlled by pre-existing relief that records tectonic deformation and erosional processes. The thickness and distribution of the upper transparent unit are controlled by long-wavelength, tectonically induced relief on the transgressive surface and hydrodynamics.