It is difficult to estimate groundwater recharge in semiarid environments, where precipitation and evapotranspiration nearly balance. In such environments, groundwater supplies are sensitive to small changes in the processes that control recharge. Numerical modeling provides the temporal resolution needed to analyze these processes but is highly sensitive to model errors. Natural chloride tracer measurements in the unsaturated zone provide more robust indicators of low recharge rates but yield estimates at coarse time scales that mask most control mechanisms. This study presents a new probabilistic approach for analyzing diffuse recharge in semiarid environments, with an application to study sites in the U.S. southern High Plains. The approach uses data assimilation to combine model predictions and chloride-based recharge estimates. It has the advantage of providing probability distributions rather than point values for uncertain soil and vegetation properties. These can then be used to quantify recharge uncertainty. Estimates of moisture flux time series indicate that percolation (or potential recharge) at the data sites is episodic and exhibits interannual variability. Most percolation occurs during intense rains when crop roots are not fully developed and there is ample antecedent soil moisture. El Niño events can contribute to interannual variability of recharge if they bring rainy winters that provide wet antecedent conditions for spring precipitation. Data assimilation methods that combine modeling and chloride observations provide the high temporal resolution information needed to identify mechanisms controlling diffuse recharge and offer a way to examine the effects of land use change and climatic variability on groundwater resources.