The unadjusted 72-h gross alpha activities in water from two wells completed in marine and alluvial deposits in a coastal southern California aquifer 40 km north of San Diego were 15 and 25 picoCuries per liter (pCi/L). Although activities were below the Maximum Contaminant Level (MCL) of 15 pCi/L, when adjusted for uranium activity; there is concern that new wells in the area may exceed MCLs, or that future regulations may limit water use from the wells. Coupled well-bore flow and depth-dependent water-quality data collected from the wells in 2011 (with analyses for isotopes within the uranium, actinium, and thorium decay-chains) show gross alpha activity in marine deposits is associated with decay of naturally-occurring ²³⁸U and its daughter ²³⁴U. Radon activities in marine deposits were as high as 2230 pCi/L. In contrast, gross alpha activities in overlying alluvium within the Piedra de Lumbre watershed, eroded from the nearby San Onofre Hills, were associated with decay of ²³²Th, including its daughter ²²⁴Ra. Radon activities in alluvium from Piedra de Lumbre of 450 pCi/L were lower than in marine deposits. Chromium VI concentrations in marine deposits were less than the California MCL of 10 μg/L (effective July 1, 2014) but δ⁵³Cr compositions were near zero and within reported ranges for anthropogenic chromium. Alluvial deposits from the nearby Las Flores watershed, which drains a larger area having diverse geology, has low alpha activities and chromium as a result of geologic and geochemical conditions and may be more promising for future water-supply development.