The Los Angeles Basin is a densely populated coastal area that significantly depends on groundwater. A part of this groundwater supply is at risk from saltwater intrusion—the impetus for this study. High-resolution seismic-reflection data collected from the Los Angeles–Long Beach Harbor Complex have been combined with borehole geophysical and descriptive geological data from four nearby ~400-m-deep continuously cored wells and with borehole geophysical data from adjacent water and oil wells to characterize the Pliocene to Holocene stratigraphy of the Dominguez Gap coastal aquifer system. The new data are shown as a north-south, two- dimensional, sequence-stratigraphic model that is compared to existing lithostratigraphic models of the Los Angeles Basin in an attempt to better understand pathways of saltwater intrusion into coastal aquifers. Intrusion of saltwater into the coastal aquifer system generally is attributed to over-pumping that caused the hydraulic gradient to reverse during the mid-1920s. Local water managers have used the existing lithostratigraphic model to site closely spaced injection wells of freshwater (barrier projects) attempting to hydraulically control the saltwater intrusion. Improved understanding of the stratigraphic relationships can guide modifications to barrier design that will allow more efficient operation. Allostratigraphic nomenclature is used to define a new sequence-stratigraphic model for the area because the existing lithostratigraphic correlations that have been used to define aquifer systems are shown not to be time-correlative. The youngest sequence, the Holocene Dominguez sequence, contains the Gaspur aquifer at its base. The Gaspur aquifer is intruded with saltwater and consists of essentially flat-lying gravelly sands deposited by the ancestral Los Angeles River as broad channels that occupied a paleovalley incised into the coastal plain during the last glacio-eustatic highstand. The underlying sequences are deformed into a broad anticlinal fold that occurs parallel to, but ~2 km north of, the axis of the Pliocene Wilmington anticline. The Dominguez sequence breaches the crest of the young anticline, cuts through the upper Pleistocene Mesa and Pacific sequences, and into the middle Pleistocene Harbor sequence. Saltwater migrates along channels within the Dominguez sequence and into the underlying sequences (composed mostly of shallow marine and tidal sands, silts, and clays) that contain the classically defined Gage and Lynwood aquifers. The newly recognized Pacific Coast Highway fault cuts through the core of this young fold and is downthrown on the northern side, thereby creating accommodation space for a thick succession of middle Pleistocene sediments that constitute the Upper Wilmington sequence. North of the Pacific Coast Highway fault, the Upper Wilmington sequence contains the classic Silverado aquifer (composed of fluviodeltaic deposits); the Silverado is the primary freshwater aquifer for the West Coast and Central Los Angeles Groundwater Basins. Pore fluid and electric log analyses show the upper part of this aquifer to be saline-intruded near the crest of the young fold. This relationship implies that some saltwater is migrating into deeper aquifers from above, across the regional unconformity that marks the base of the Harbor sequence (ca. 240–270 ka). This sequence-stratigraphic model provides new insight into the potential flow paths for saltwater intrusion, and as such, should allow improved characterization of fluid flow that will aid in transport model studies and in managing groundwater resources.