Gold mining stands out as a primary industrial operation significantly affecting the environment, underscoring the urgency of developing strategies to enhance environmental stewardship in the impacted areas. In areas directly or indirectly affected by emissions of hazardous substances like As, Cd, Pb, and Cr, these strategies are crucial for informed decision-making. Zoning the spatial distribution of these elements and using indices and pollution bioindicators can create a diagnostic and remedial tool to address pollution concerns effectively. The aim of this study is to apply environmental zoning in three gold-mining-affected municipalities in Antioquia, Colombia. The zoning considers various factors, including i) levels of potentially toxic elements, ii) contamination indices, and iii) bioindicators. Geospatial analysis was employed to create maps illustrating the distribution of potential toxic elements, along with the indices and bioindicators utilized. The results show that the concentrations of potentially toxic elements were the lowest, even below the reference values for non-contaminated soils, in the municipality of Yalí. In contrast, most samples from Puerto Berrío and Buriticá revealed amounts of potentially toxic elements higher than the standards for uncontaminated soils. In particular, the highest contamination values for the elements Cd, Pb, and Cr were found in Puerto Berrío. The correlation study shows that concentrations of potentially toxic elements, pollution indices, and bioindicators have a substantial association (P < 0.05) (r > 0.67). The municipalities can be categorized into three zones: a highly polluted area needing remediation, a moderately polluted zone requiring natural restoration monitoring, and a low-contamination region needing conservation efforts. Overall, this zoning proposal can help competent authorities enhance environmental management strategies.