This article provides an assessment of the negative impact of a tailings storage facility (TSF) on surface and groundwaters. Impact assessments for the settling ponds were conducted in several stages to establish the migration of pollutants outside the TSF. Sample selection analysis and a subsequent evaluation of the current situation were used to identify the possible pollutant infiltration points, find pollutant migration patterns, and establish respective technogenic hydrochemical pollution halos, reaching outside the sanitary protection zone of the plant. The composition of tailings and waters in the TSF and the drainage wells was studied to describe the erosion mechanism behind TSF elements migration into the dilution ponds. A water treatment method is described, based on the use of slaked lime. This method reduces the concentration of heavy metals in the ponds and enables further use of the waste generated as a backfill material. Balancing ponds have been identified as the main sources of acidic drainage waters deposition and migration into surface and groundwaters. The article identifies the formation mechanism for such waters at the TSF. Various treatment methods were investigated, aimed to eliminate the pollution problem. The need to increase the pH value of acidic waters and reduce the contents of dissolved elements in model solutions through precipitation was set as the main selection criterion. A mixture of Ca(OH)2 + NaOH (3 : 1) was selected as the preferred option as it allows raising the pH value to 5–6, causes the formation of smaller amounts of sediment, and reduces the amount of pollutants to a suitable level for the plant. The use of a flocculant (polyacrylamide) is an important factor in this treatment method since it reduces the settling time from 22 to 4 hours.