Acid mine drainage (AMD) is an environmental concern that needs to be addressed by some mining industries because of its high concentrations of metals and acidity that destroy affected ecosystems. Its formation typically persists beyond the operating life of a mine site. Its management is even more challenging for sites that are abandoned without rehabilitation. In this study, a legacy copper–gold mine located in Sto. Niño, Tublay, Benguet, Philippines, generating a copper- and manganese-rich AMD (Cu, maximum 17.2 mg/L; Mn, maximum 2.90 mg/L) at pH 4.59 (minimum) was investigated. With its remote location inhabited by the indigenous people local community (IPLC), a novel limestone-based hybrid passive treatment system that combines a limestone leach bed (LLB) and a controlled modular packed bed reactor (CMPB) has been developed from the laboratory and successfully deployed in the field while investigating the effective hydraulic retention time (HRT), particle size, and redox conditions (oxic and anoxic) in removing Cu and Mn and increasing pH. Laboratory-scale and pilot-scale systems using simulated and actual AMD, respectively, revealed that a 15 h HRT and both oxic and anoxic conditions were effective in treating the AMD. Considering these results and unsteady conditions of the stream in the legacy mine, a hybrid multi-stage limestone leach bed and packed bed were deployed having variable particle size (5 mm to 100 mm) and HRT. Regular monitoring of the system showed the effective removal of Cu (88.5%) and Mn (66.83%) as well as the increase of pH (6.26), addressing the threat of AMD in the area. Improvement of the lifespan of the system needs to be addressed, as issues of Cu-armoring were observed, resulting in reduced performance over time. Nonetheless, the study presents a novel technique in implementing passive treatment systems beyond the typical treatment trains reported in the literature.