Springs and groundwater seeps along the South Rim of the Grand Canyon serve an important function for the region’s ecosystems, residents (both human and wild animal), and economy. However, these springs and seeps are potentially vulnerable to contamination, increased groundwater extraction, or reduced recharge due to climate change. Protection of South Rim groundwater resources requires improved understanding of the regional groundwater system. In this study, statistical methods are used to investigate δ2H and δ18O in precipitation, surface water, and groundwater. A mixing model for δ18O is developed using statistically distinct seasonal end-members represented by modeled winter (Nov-Apr.) precipitation and summer (May-Oct.) surface water run-off. The calculated fraction of winter recharge (Fwin) indicates that South Rim groundwater is primarily sourced from snow-melt and winter rains with an average Fwin of 0.97 ± 0.09. Groundwater sourced from the highest elevations of the study area are more depleted than the winter end-member suggesting values of Fwin are overestimated or a meaningful portion of recharge occurs at lower elevations. Lower elevation recharge from the Coconino Plateau is supported by consistent spatial trends in δ2H and δ18O with respect to longitude, Fwin values less than 0.9 for 9 of the 50 samples, and age tracer data indicating young groundwater discharging from springs which is distinct from old groundwater observed in the regional flow system. These results suggest a new conceptual model is needed to account for recharge sources from low elevation and summer precipitation. Results imply resource managers need to reconsider current land-use and water management practices on the South Rim to protect future water quantity and quality.