The San Diego County Water Authority has been working to diversify its water supplies and there is an interest in the potential utilization of the Mission Valley aquifer as a source. Previously, groundwater in San Diego County has largely been ignored with only a few studies attempting to identify characteristics of the Mission Valley aquifer. In order to properly manage the Mission Valley aquifer, information about sources of groundwater recharge are necessary. This project answers this question by quantifying the flow pathways delivering water into the aquifer. Each potential source of recharge was investigated by determining their unique 18O and 2H isotopic “fingerprints” and comparing them to that of groundwater. These fingerprints were then used as endmembers in End-Member Mixing Analysis (EMMA), which solves a system of equations using the least squares method to produce percentages of each source contributing to recharge. To determine endmembers, samples of baseflow, precipitation, and stormflow from 8 storm events were taken from three different streams that may contribute to aquifer recharge. The samples were then analyzed for their isotopic composition. Results of EMMA indicate that during storm events, streamflow in the main stem of the San Diego River is initially discharged with precipitation, then groundwater return flow is dominant the rest of the storm. Overall stormflow composition of the San Diego River is a mixture pre-event evaporated baseflow and non-evaporated baseflow, characteristic of groundwater. Stormflow composition in two tributaries of the San Diego River was reflective of precipitation, indicating discharge produced during storm events is attributed to rainfall input. EMMA ran on each individual groundwater sample determined that groundwater was recharged through the infiltration of streamflow, with 2/3rds from non-evaporated streamflow occurring during storm events and 1/3rd from evaporated baseflow. Groundwater composition did not vary seasonally, suggesting long residence times.