Endmember mixing analysis (EMMA) is often used by hydrogeochemists to interpret the sources of stream solutes, but variations in stream concentrations and discharges remain difficult to explain. We discovered that machine learning can be used to highlight patterns in stream chemistry that reveal information about sources of solutes and subsurface groundwater flowpaths. The investigation has implications, in turn, for the balance of CO2 in the atmosphere. For example, CO2-driven weathering of silicate minerals removes carbon from the atmosphere over ∼106-year timescales. Weathering of another common mineral, pyrite, releases sulfuric acid that in turn causes dissolution of carbonates. In that process, however, CO2 is released instead of sequestered from the atmosphere. Thus, understanding long-term global CO2 sequestration by weathering requires quantification of CO2- versus H2SO4-driven reactions. Most researchers estimate such weathering fluxes from stream chemistry, but interpreting the reactant minerals and acids dissolved in streams has been fraught with difficulty. We apply a machine-learning technique to EMMA in three watersheds to determine the extent of mineral dissolution by each acid, without pre-defining the endmembers. The results show that the watersheds continuously or intermittently sequester CO2, but the extent of CO2 drawdown is diminished in areas heavily affected by acid rain. Prior to applying the new algorithm, CO2 drawdown was overestimated. The new technique, which elucidates the importance of different subsurface flowpaths and long-timescale changes in the watersheds, should have utility as a new EMMA for investigating water resources worldwide.