Without treatment, the harmful effects of acid mine drainage (AMD) lead to the destruction of surrounding ecosystems, including serious health impacts to affected communities. Active methods, like chemical neutralization, are the most widely used approach to AMD management. However, these techniques require constant inputs of energy, chemicals, and manpower, which become unsustainable in the long-term. One promising and sustainable alternative for AMD management is to use passive treatment systems with locally available and waste-derived alkalinity-generating materials. In this study, the treatment of synthetic AMD with laterite mine waste (LMW), concrete waste, and limestone in a successive process train was elucidated, and the optimal process train configuration was determined. Six full factorial analyses were performed following a constant ratio of 0.75 mL AMD/g media with a 15-min retention time. The evolution of the pH, redox potential (Eh), total dissolved solids (TDS), heavy metals concentration, and sulfates concentrations were monitored as the basis for evaluating the treatment performance of each run. LMW had the highest metal and sulfates removal, while concrete waste caused the largest pH increase. A ranking system was utilized in which each parameter was normalized based on the Philippine effluent standards (DENR Administrative Order (DAO) 2016–08 and 2021–19). Run 4 (Limestone-LMW-Concrete waste) showed the best performance, that is, the pH increased from 1.35 to 8.08 and removed 39% Fe, 94% Ni, 72% Al, and 52% sulfate. With this, the process train is more effective to treat AMD, and the order of the media in treatment is significant.