Background.Water quality in the Marilao-Meycauayan-Obando river system (MMORS) of Bulacan, the Philippines, is of great concern due to the pollution load from local industries. The river system is currently used as a source of water for the aquaculture industry in Bulacan.Objectives.In order to address organic and heavy metal pollution, several remediation strategies were tested in aquaculture ponds along the river system. Strategies such as phytoremediation (vetiver grass pontoons), application of probiotics and zeolite (with filtration as pre-treatment) were utilized in ponds to decrease or remove toxic pollutants in water and sediments.Methods.Two sites were chosen as the pilot remediation sites – ponds in Barangay Nagbalon, Marilao and Barangay Liputan, Meycauayan, Bulacan. Pond bottom preparation was done to improve the condition of the pond bottom sediments before stocking by adding zeolite. Physicochemical parameters of water such as dissolved oxygen (DO), temperature, pH, salinity, ammonia, phosphate, biochemical oxygen demand (BOD) and chemical oxygen demand (COD) were monitored throughout the culture period. Heavy metals in sediments and fish were monitored. Fish parameters such as average body weight and feed conversion ratio were determined.Results.The DO levels were below recommended levels in the morning and reached a supersaturated level in the afternoon. Ammonia and COD levels were above recommended limits. A decreasing trend was observed for ammonia levels in treatment ponds. In terms of the growth of milkfish, the pond with probiotics showed the highest growth and better feed conversion ratio in Nagbalon and in the phytoremediation pond in Liputan. Percentage survival of milkfish was much higher at Liputan. Copper, chromium, lead and manganese were detected in pond sediments. After application of zeolite, there was a decrease in lead levels throughout the culture period.Conclusions.The different remediation studies were compared in terms of cost, effectivity and application and phytoremediation (vetiver grass pontoons) was determined to be the most cost-effective remediation strategy.Competing Interests.The authors declare no competing financial interests.