As drinking-water scarcity grows worldwide, we need to improve predictions of the quantity and quality of our water resources. An overarching problem for model improvement is that we do not know the geological structure of aquifers in sufficient detail. In this work, we demonstrate that mineral-water reactions imprint structure in the subsurface that impacts the flow and transport of some chemical species. Specifically, pyrite, a ubiquitous mineral, commonly oxidizes and depletes in the upper layers of the weathering profile in most humid watersheds, only remaining at depths of meters. We hypothesize that variations in concentrations (C) of pyrite-derived sulfate released into rivers as a function of discharge (q) reflect the rate-limiting step and depth of pyrite-oxidizing layers. We found that log C − log q behaviors thus differ in small and large watersheds in the Susquehanna River Basin as well as in selected watersheds in the Western United States. Although coal mining changes pyrite oxidation from closed to open system with respect to O2, patterns in stream chemistry as a function of discharge are consistent with deep and shallow pyrite oxidation zones in small and large watersheds respectively. Therefore, understanding the subsurface patterns of mineral reactions and how they affect the architecture of aquifers will elucidate patterns of changing river chemistry and our ability to manage water resources in the future under accelerated land use and climate change.