A limited understanding of how extreme weather events affect groundwater hinders our ability to predict climate change impacts in drylands, where channel transmission losses are often the primary recharge mechanism. In this study, we investigate how potential changes to precipitation intensity and temperature will affect the water balance of a typical first-order, arid watershed located in the Chihuahuan Desert. We utilize a process-based hydrologic model driven by stochastically-downscaled simulations from a set of climate models, emissions scenarios, and future periods. Across many simulations, the average daily storm size is the primary factor that controls transmission losses with larger precipitation amounts increasing channel infiltration while simultaneously decreasing land surface evapotranspiration. Extreme events (>25 mm d−1) that account for less than 30% of the annual precipitation, contribute almost 50% of the focused recharge. As a result, climatic changes leading to larger, less frequent storms will result in higher channel transmission losses in arid regions.