We investigated how natural sources of metals might obscure the assessment of abandoned mined lands.  Our sampling design targeted small catchments underlain by monolithic rock types which allowed the development of biological and geochemical baselines based on a single lithology. By accounting for geologic sources of metals to the environment, we were able to distinguish the environmental effects caused by weathering of different mineral deposits.  This sampling design provided geochemical and biological baselines distinct from reference site selection based on disturbance regime.  Hydrothermal alteration and deposit type were important determinants of water and sediment quality as well as aquatic community structure in both mined and unmined catchments.  Natural weathering of certain rock types virtually excluded metal-sensitive taxa from streams whereas some mined rock types supported a robust benthic community and had water and sediment quality ≤ risk thresholds for metals.  We determined that both ore deposit type and the form of mineralization are important predictors of mine effects on the environment.  Our sampling approach can be used to more accurately predict effects of historical and future mining on the environment in the Rocky Mountains and the American west.