Discharge of deeply sourced groundwater to streams is difficult to locate and quantify, particularly where both discrete and diffuse discharge points exist, but diffuse discharge is one of the primary controls on solute budgets in mountainous watersheds. The noble gas helium is a unique identifier of deep groundwater discharge because groundwater with long residence times is commonly enriched in helium. In this study, a portable mass spectrometer was used to measure longitudinal variation in dissolved helium concentrations in two mountainous rivers at high spatial resolution not feasible with traditional sampling techniques. Helium profiles were then simulated using a mass-balance model to quantify longitudinal variation in groundwater discharge to the receiving rivers. Results indicate helium concentrations were enriched by multiple orders of magnitude above atmospheric equilibrium in both rivers and that this persisted for up to 18 km below observed pulse inputs in the Colorado River. Helium mass-balance models match observed longitudinal patterns with the exception of sharp initial increases in helium observed in the rivers. Increased longitudinal groundwater discharge rates correspond to mapped geologic structures in both watersheds that likely transport deep geothermal water. Models show variable sensitivity to spatial assignment of input variables representing the groundwater source, illustrating the importance of collecting data from discrete groundwater discharges where possible. The methodology shows promise for field experiments designed to assess air–water exchange rates and to quantify total groundwater discharge from a combination of discrete and diffuse sources.