© 2015, The Author(s). Groundwater has provided 50–90 % of the total water supply in Antelope Valley, California (USA). The associated groundwater-level declines have led the Los Angeles County Superior Court of California to recently rule that the Antelope Valley groundwater basin is in overdraft, i.e., annual pumpage exceeds annual recharge. Natural recharge consists primarily of mountain-front recharge and is an important component of the total groundwater budget in Antelope Valley. Therefore, natural recharge plays a major role in the Court’s decision. The exact quantity and distribution of natural recharge is uncertain, with total estimates from previous studies ranging from 37 to 200 gigaliters per year (GL/year). In order to better understand the uncertainty associated with natural recharge and to provide a tool for groundwater management, a numerical model of groundwater flow and land subsidence was developed. The transient model was calibrated using PEST with water-level and subsidence data; prior information was incorporated through the use of Tikhonov regularization. The calibrated estimate of natural recharge was 36 GL/year, which is appreciably less than the value used by the court (74 GL/year). The effect of parameter uncertainty on the estimation of natural recharge was addressed using the Null-Space Monte Carlo method. A Pareto trade-off method was also used to portray the reasonableness of larger natural recharge rates. The reasonableness of the 74 GL/year value and the effect of uncertain pumpage rates were also evaluated. The uncertainty analyses indicate that the total natural recharge likely ranges between 34.5 and 54.3 GL/year.