Climate change has a pronounced effect on water resources in many semiarid climates, causing populated areas such as San Diego County (USA), to become more vulnerable to water shortages in the coming decades. To prepare for decreased water supply, San Diego County is adopting policies to decrease water use and to develop additional local sources of water. One new local source of freshwater is produced by a desalination facility that purifies brackish groundwater from the coastal San Diego Formation. This formation has been studied extensively onshore, but little is known about the geology or groundwater quality offshore in the adjacent continental shelf. Because most groundwater systems are interconnected and complex, further analysis is needed to identify offshore geology, possible sequestration of freshwater in the shelf, and potential pathways for saltwater intrusion. This comprehensive understanding is important because seawater intrusion may limit use of the San Diego Formation and longevity of desalination facilities. Controlled-source electromagnetic methods are uniquely suited to detecting offshore groundwater as they are sensitive to changes in pore fluids such as the transition from fresh to brackish groundwater. This paper describes results from surface-towed electromagnetic surveys that mapped the pore-fluid salinity and possible fluid pathways in the continental shelf off the coast of San Diego. The results indicate a considerable volume of fresh-to-brackish groundwater sequestered in the shelf, both in continuous lenses and isolated pockets, that appear influenced by fault systems and shallow stratigraphy.