Environmental hazards associated with mine waste dumps, particularly the formation of acid mine drainage (AMD) and the mobilization of toxic metals into surrounding water bodies and soils, represent some of the most critical challenges in metal mining operations. This study presents an integrated approach, supported by numerical modeling, to control AMD generation and limit contamination of nearby water resources. Aligned with the principle of "prevention prior to remediation," source control strategies were defined to minimize the interaction between water, atmospheric oxygen, and sulfide-bearing materials. Specifically, measures such as dry cover systems composed of compacted clay, geosynthetics, and recycled industrial materials, along with stratified encapsulation of acid-generating waste within neutralizing agents, were simulated using hydrogeochemical models. A laboratory-scale physical model was developed and implemented to validate the numerical predictions. The results showed that the combination of a 0.15 m thick dry cover and encapsulation process reduced oxygen ingress and AMD formation by up to 52%. Additionally, the pH of the leachate increased from 2.3 to 6.4, while iron and lead concentrations decreased by approximately 63% and 48%, respectively. These findings provide practical guidance for improving the environmental design and management of mine waste dumps and inform more effective strategies for protecting water resources and aquatic ecosystems in mining environments.