It is often difficult to determine the sources of solutes in streams and how much each source contributes. We developed a new method of unmixing stream chemistry via machine learning. We found that sulfate in three watersheds is related to groundwater flowpaths. Our results emphasize that acid rain reduces a watershed's capacity to remove CO₂ from the atmosphere, a key geological control on climate. Our method will help scientists unmix stream chemistry in watersheds where sources are unknown.