For more than twenty years, the province of Marinduque has felt the negative effects brought by the previous mining operation of the Marcopper Mining Corporation and the 1996 Marcopper mining disaster that contaminated the Boac River System. The 1996 Marcopper mining disaster was the most significant event in the chain of events that transpired with MMC’s operation on the island. A total of eleven mining and environmental-related policies were examined which exhibited both critical juncture and path dependence, wherein it could be associated with the mining disasters that transpired in Marinduque. The identified challenges in the study were grouped into three main areas: environment, health, and governance — all of which impede the long-term rehabilitation of the Boac River. From the challenges identified, problem-fit programs and policy reform recommendations were formulated that could be utilized in future policy and program creations or revisions. This study assessed the challenges related to the policies and prospects for the long-term rehabilitation of the Boac River with the 1996 Marcopper mining disaster that could serve as a reference for future mining policy reform mechanisms.