High-resolution CHIRP seismic surveys were conducted offshore San Diego to understand channel incision, erosion, and deposition throughout a glacial cycle. Eustasy controls deposition and erosion across the local coastal plain and shelf, whereas tectonic deformation controls channel orientation, sediment dispersal pathways, and preservation potential. Sub-parallel, northwest trending fault zones on and offshore San Diego create a structural horst that is bound to the west and east by extensional downdropped faults. The horst creates a bathymetric and topographic high, subaerially expressed as the Point Loma Peninsula, and is known to be uplifting at the regional rate of ~0.13-0.14 mm/yr. To the east of the bathymetric high, vertical offset along southern splays of the Rose Canyon Fault Zone form a downdropped basin in San Diego Bay and the San Diego Bight. Sediments mantling an MIS 4 erosional surface are interpreted as fluvial and estuarine deposits emplaced during MIS 3. These sediments and underlying units were subsequently truncated and incised during the Last Glacial Maximum (LGM - MIS 2). The preservation of deposits and erosional surfaces is more prevalent to the east of the Southern Spanish Bight Fault. In this region, the Southern Spanish Bight Fault vertically offsets the transgressive surface by an average of ~0.9 m and the interpreted MIS 4 erosional surface by ~4.7 m. Observations of paleo-channelization across the shelf and modern deposition of Holocene sediments indicates that the erosion resistant Cretaceous lithology of the Point Loma Peninsula acts as a drainage divide during periods of low sea level and as a circulation divide during periods of high sea level. The regional tectonic structure, in conjunction with the erosion-resistant character of the local Cretaceous lithology, controls channel architecture, sediment transport and accumulation, as well as nearshore circulation in the San Diego Bight.