The Portuguese Institute for Water has started a survey of possible impact zones on the water quality of watersheds, and a copper extraction industrial process using a dam for the dumping of mining waste is being carefully monitored. This earth dam is located in a tributary of the main river in a region of highly variable hydrologic regime (with torrential features) and has to be controlled to avoid overtopping. The channeling of most of the overland flow to the reservoir has reduced the watershed drainage area, and some of the water at the surface of the reservoir might be pumped and treated in a special mine water treatment plant before being returned to the river downstream in alert situations. These two options require validation both for the water balance in the reservoir and for specific in-stream flow requirements. The complexity of the processes involved was better conceptualized through a desagregated hydrological modeling in a GIS environment.