Semi-arid and arid rivers typically exhibit increasing salinity levels downstream, a trend often attributed to irrigated agriculture, primarily due to evapotranspiration. In contrast, the results of our investigations in one salinized river suggest that geological sources of salt added by groundwater discharge are more important than agricultural effects. We performed detailed synoptic sampling of the Upper Rio Grande–Rio Bravo, an arid-climate river with significant irrigated agriculture, and identified a series of salinity increases localized at the distal ends of sedimentary basins. Using Cl/Br, Ca/Sr, 87Sr/86Sr, and 36Cl/Cl ratios and δ234U values as environmental tracers, we show that these increases result from localized discharge of high-salinity groundwater of a sedimentary brine source. These groundwater fluxes, while very small (<1 m3s−1), are the dominant solute input and, combined with downstream evapotranspirative concentration, result in salinization. Furthermore, 36Cl/Cl ratios and δ234U values for these brines are close to secular equilibrium, indicating brine ages on the order of millions of years. The recognition of a substantial geologic salinity source for the Rio Grande implies that alternative salinity management solutions, such as interception of saline groundwater, might be more effective in reducing salinity than changes in agricultural practices.