Sulfide mining wastes may lead to severe environmental and human health risks. This study aims to use geochemical and ecotoxicological indicators for the assessment of the ecological risks of potentially toxic elements (PTEs) in the San Quintín mining group to categorize wastes prior to mining restoration. Ecotoxicity was evaluated using crustacean (Dahpnia magna, Thamnocephalus platyurus) and algae (Raphidocelis subcapitata) bioassays. The geochemical and mineralogical results suggested that the mining residues underwent intense weathering processes, with active processes of acidity generation and metal mobility. Total PTEs concentrations indicated that the mining materials were extremely polluted, with Pb, Zn and Cd geoaccumulation index (Igeo) values higher than 5 in more than 90% of the samples. The pollution load index (PLI) showed average values of 18.1, which classifies them as very highly polluted. The toxicity tests showed a higher toxicity for plants than crustaceans, being the highest values of toxicity related to toxic elements (Pb, Cd and Zn), electrical conductivity and to pH. This paper presents for the first time the combination of indices in the categorization of mining waste prior to its restoration. The combination of them has made it possible to categorize the waste and adapt the restoration and remediation procedures.