Prior to World War II, the City of San Diego, California, extracted millions of gallons of high-quality groundwater daily from alluvial gravels in the lower San Diego River Valley that have since become contaminated with brackish water and hydrocarbons. The origin of this brackish groundwater and of the Quaternary sedimentary geology of the valley is interpreted through archived reports, journal articles, U.S. Geological Survey data, and samples from new city wells in the alluvial gravels. Eocene sediments were inundated by seawater during the last interglacial period (ca. 120 ka), when sea levels were ∼19 ft (6 m) higher than present levels. The brackish groundwater present in these Eocene sediments appears to be relict seawater from this inundation. We hypothesize that the city’s pre–World War II well field—referred to herein as the Mission Valley Aquifer—was a buried channel gravel created following the Last Glacial Maximum of the Pleistocene Epoch (∼20 ka). As such, it would have been similar to other long (∼11 km, 7 mi) buried channel gravels along the southern Californian coast described in previous reports. We present evidence of groundwater freshening of the Eocene sedimentary rock that has led to increasing total dissolved solids in the Mission Valley Aquifer, which acts as a high-permeability drain for the valley. Freshening occurs as a Ca-HCO3 groundwater replaces a Na-Cl water, which we propose was derived from the marine inundation of 120 ka.