Abstract. The coastal-plain aquifer that underlies the San Diego City metropolitan area in southern California is a groundwater resource. The understanding of the region-wide water balance and the recharge of water from the high elevation mountains to the east needs to be improved to quantify the subsurface inflows to the coastal plain in order to develop the groundwater as a long term resource. This study is intended to enhance the conceptual understanding of the water balance and related recharge processes in this arid environment by developing a regional model of the San Diego region and all watersheds adjacent or draining to the coastal plain, including the Tijuana River basin. This model was used to quantify the various components of the water balance, including semi-quantitative estimates of subsurface groundwater flow to the coastal plain. Other approaches relying on independent data were used to test or constrain the scoping estimates of recharge and runoff, including a reconnaissance-level groundwater model of the San Diego River basin, one of three main rivers draining to the coastal plain. Estimates of subsurface flow delivered to the coastal plain from the river basins ranged from 12.3 to 28.8 million m3 yr−1 from the San Diego River basin for the calibration period (1982–2009) to 48.8 million m3 yr−1 from all major river basins for the entire coastal plain for the long-term period 1940–2009. This range of scoping estimates represents the impact of climatic variability and realistically bounds the likely groundwater availability, while falling well within the variable estimates of regional recharge. However, the scarcity of physical and hydrologic data in this region hinders the exercise to narrow the range and reduce the uncertainty.