This paper addresses the modelling of the processes associated with acid mine drainage affecting the Trimpancho River basin, chosen for this purpose because of its location and paradigmatic hydrological, geological, mining and environmental contexts. By using physical-chemical indicators it is possible to define the contamination degree of the system from the perspective of an entire river basin, due to its reduced dimension. This allows an exhaustive monitoring of the study area, considering the particularity that the stream flows directly into a water dam used for human supply. With such a perspective, and in order to find global solutions, the present study seeks to develop methodologies and tools for expeditious and accurate diagnosis of the pollution level of the affected stream that feeds the water reservoir. The implemented methodology can be applied to other water systems affected by similar problems, while the results will contribute to the development of the state of the art in a representative basin of the Iberian Pyrite Belt, whose pollutants' contributions are incorporated into the reservoir.