Effective waste rock management is a crucial aspect of long-term mine planning and production scheduling. When waste management is not considered during the life of mine production schedule optimization, it leads to an inaccurate assessment of the financial outcomes of the related mining complex. This oversight can be particularly problematic when dealing with waste rock that is potentially acid-generating (PAG), as it introduces the risk of significant treatment costs related to rehabilitation, primarily due to acid rock drainage (ARD). To prevent or mitigate ARD, proactive measures, such as encapsulating PAG material with non-acid-generating (NAG) material, are essential. Furthermore, stricter legislation reinforces the necessity to restore mining sites to an acceptable post-mining condition, using ongoing reclamation to ensure environmental stability and reduce long-term liabilities. This work integrates waste management and progressive rehabilitation into the simultaneous stochastic optimization of mining complexes, employing gradual encapsulation of PAG material to promote progressive reclamation, thereby reducing long-term environmental and financial liabilities. Uncertainties in acid generation are addressed using geostatistical simulations of the rock's geochemical properties of the mine deposit considered. A case study at a copper-gold mining complex demonstrates that incorporating waste management by using progressive encapsulation leads to minimal financial impact.