Groundwater and surface water interactions in mountain catchments occur at much larger scales than previously recognized. Because mountains are "water towers" and provide much of the water needed to adjacent low lands, it is important to understand these interactions to accurately assess water fluxes within a mountain system. This dissertation presents an approach using several environmental tracers to identity source waters, establish groundwater residence times, and identify groundwater discharge locations in the Merced River basin between Yosemite Valley and El Portal.  ³⁶Cl and Cl^- were used to identify source waters and to characterize their discharge contributions to stream flow in the Upper Merced River. Near-surface water was found to be the largest endmember. Low-Cl^- evapotranspired water was second, and high-Cl^- was third. Near-surface water was primarily released during snowmelt, but snow was not an obvious endmember. Snow and near-surface water had Cl^- concentrations <0.25 mgL^-1, but the ³⁶Cl/Cl in near-surface water was much greater than in snow (i.e. ~10000x10^-15 compared to <306x10^-15). The elevated ratio is likely from bomb-pulse ³⁶Cl still circulating in the biosphere. One possible mechanism may be retention of bomb-pulse ³⁶Cl into organic matter, which later remineralizes, providing Cl^- to near-surface water. This process would indicate that retention of organochlorines has timescales up to 40-50 years. Low-Cl^- evapotranspired water was only observed in tributaries, during baseflow, and in Yosemite Valley groundwater samples. High-Cl^- groundwater was observed in El Portal groundwater, a spring at the top of Yosemite Valley, and the Merced River during baseflow. Although its contributions to stream flow is lowest compared to other endmembers, its flow rates are more stable.  Low-Cl^- groundwater is characterized by ³H/³He ages between 7 and 28 yrs, 0-50% premodern water, and ⁴He_RAD ranging between 1.0x10^-8 to 5.7x10^-8 cm³ (STP) g^-1. High-Cl^- groundwater is characterized by ³H/³He ages between 23 and 49 yrs, >75% premodern water, and ⁴He_RAD ranging between 6.7x10^-7 and 1.6x10^-6 cm³(STP) g^-1. ³H/³He ages in a spring and a groundwater well increase ~10 to 20 yrs, from snowmelt to baseflow.  ²²²Rn in the Merced River along the reach in Yosemite Valley remains spatially uniform in comparison to downstream of Yosemite Valley, which suggests a constant groundwater flux. Downstream of Yosemite Valley groundwater discharge to the river is typically much lower than in Yosemite Valley, but there are point-source locations of elevated groundwater discharge occurring at fracture zones. The differences between these two river reaches appear to be controlled by the amount of alluvium (i.e. Yosemite Valley consists of ~300 m of alluvium in comparison to <30 m of alluvium downstream). This study improves our understanding of how stream flow is generated in snowmelt-dominated catchments and how climate change may affect stream flow regime. The small contributions and young ages of groundwater mixing with surface water in the Merced River basin, suggests that the Sierra Nevada may be even more vulnerable to the climate change than other mountain systems.