Warden Gulch is a high-mountain stream located in Summit County, Colorado, and is contaminated with acid mine drainage from multiple mines in its watershed. This thesis develops a framework which can be used to identify the most significant source of contamination in a watershed. The framework follows a set of tasks which estimates the governing parameters and processes of the watershed, quantifies stream chemistry and metal loadings along the stream, simulates the transport of contaminants within the watershed, and prioritizes mine sites through application of the backward probability theory. When contamination is observed in an aquifer, backward location and travel time probability density functions can be used to efficiently identify prior positions and release times of contamination, respectively. These functions are used to prioritize mine sites in the Warden Gulch watershed, with the highest priority given to the site whose remediation leads to the most substantial improvement in water quality.