Illegal gold mining is on the rise in the tropical Andes. The Santiago-Cayapas watershed is located in the north of the Pacific basin of Ecuador, in the Chocó biogeographical region. It is recognized for its high biodiversity, as 62 fish species have been described in the area, and because it contains two of the largest protected areas in the Pacific coast of Ecuador: the mangroves of the Cayapas and Mataje Rivers and the Cotacachi-Cayapas Ecological Reserve. Open-pit gold mining has been described in the area since 2006 and most mining fronts operate illegally and lack any environmental control. Heavy-metal concentrations and fish communities were studied in streams that drain active and abandoned mines, in larger rivers located downstream of the mined areas and in control sites without mining activities. Open-pit mining causes a reduction of dissolved oxygen concentrations and an increase of water temperature, turbidity, and concentrations of Al, Cr, Co, Cu, Fe, Mn, and V. Fish abundance decreased in streams that drain active mines, however, metrics of taxonomic diversity remain unchanged among the study sites. The response of fish communities to open-pit gold mining was complex and driven by the pollution tolerance of each species, the presence of specific adaptions to turbid waters, and changes in the fishing pressure as locals avoid fishing activities in mined areas. Finally, streams that drain abandoned mines showed chemical characteristics, metal concentrations, and fish communities that were similar to control sites, but maintained higher water temperatures than control sites.