 Groundwater in the San Juan Creek basin, also referred to as the "San Juan Creek Groundwater Basin", has a total volume of roughly 900,000 acre feet (1.1 × 109 m3). (California State Water Resources Control Board, 1977.) Natural groundwater recharge in the San Juan basin is estimated to be roughly 160,000 acre feet (200,000,000 m3) per year historically, mostly from precipitation. This amount has been reduced due to extensive development of the lower segment of the watershed, which is continuing to reduce the amount of open ground that can potentially serve in groundwater recharge. Artificially sourced water from irrigation and other uses is responsible for recharging roughly 37,500 acre feet (46,300,000 m3) annually. The watershed is essentially split into half by the Christianitos and Mission Viejo fault zones, which result in the division of the "Upper" and "Lower" groundwater basins. The groundwater mostly lies in alluvium, which ranges from a depth of 200 feet (61 m) in the lower watershed to mostly none in the upper reaches of the watershed.
