This paper provides an overview of the impacts of mining-related environmental liabilities on humans, soils, sediments, surface water and groundwater across various mining districts in Zacatecas, Mexico. An analysis has been carried out on the areas of the state most affected by the presence of potentially toxic elements (PTEs) such as arsenic, lead, cadmium, copper, chromium and zinc, identifying priority areas for environmental assessment and remediation. Likewise, a review of the concentrations of PTEs reported in different environmental matrices of the state’s mining areas with the presence of environmental liabilities was carried out, most of which exceed the maximum permissible limits established by Mexican and international regulations, generating an environmental risk for the populations near these districts due to their potential incorporation into the food chain. Additionally, this study explores research focused on the biostabilization of PTEs using microorganisms with specific metabolic activities. Phytoremediation is presented as a viable tool for the stabilization and elimination of PTEs, in which endemic plants from arid–semi-arid climates have shown favorable results in terms of the phytostabilization and phytoextraction processes of the PTEs present in mining waste.