Abstract Historical production of metals in the western United States has left a legacy of acidic drainage and toxic metals in many mountain watersheds that are a potential threat to human and ecosystem health. Studies of the effects of historical mining on surface water chemistry and riparian habitat in the Animas River watershed have shown that cost-effective remediation of mine sites must be carefully planned. of the more than 5400 mine, mill, and prospect sites in the watershed, ∼80 sites account for more than 90% of the metal loads to the surface drainages. Much of the low pH water and some of the metal loads are the result of weathering of hydrothermally altered rock that has not been disturbed by historical mining. Some stream reaches in areas underlain by hydrothermally altered rock contained no aquatic life prior to mining. Scientific studies of the processes and metal-release pathways are necessary to develop effective remediation strategies, particularly in watersheds where there is little land available to build mine-waste repositories. Characterization of mine waste, development of runoff profiles, and evaluation of ground-water pathways all require rigorous study and are expensive upfront costs that land managers find difficult to justify. Tracer studies of water quality provide a detailed spatial analysis of processes affecting surface- and ground-water chemistry. Reactive transport models were used in conjunction with the best state-of-the-art engineering solutions to make informed and cost-effective remediation decisions. Remediation of 23% of the high-priority sites identified in the watershed has resulted in steady improvement in water quality. More than $12 million, most contributed by private entities, has been spent on remediation in the Animas River watershed. The recovery curve for aquatic life in the Animas River system will require further documentation and long-term monitoring to evaluate the effectiveness of remediation projects implemented.