Manila Bay is considered as one of the best locations to experience sunset, visitation for relaxation, and a place for gathering. However, the constant draining and dump coming from different industrial sectors has developed to a bay which constitutes to high level of pollutions. The need to address the issue with regards to water body pollution has been underexplored. The paper investigates several fecal coliform reduction methods: the use of secondary and tertiary treatments like sand filtration and UV disinfection processes bolstering activated sludge processes, membrane bioreactor technology systems, and intermittent filtering. The following methods were examined to resolve Manila Bay’s Bathing Beaches’ high fecal coliform levels. The use of intermittent filtering with the filter media of unsorted sand yielded the highest reduction rate of 6.3 log₁₀ compared to common activated sludge processes averaging only 0.38 log₁₀. The mitigation of the bays could potentially reduce ecological and environmental problems. Food, water, and energy are primary concerns for a country’s sustainability. With the involvement of pollution, the rise of capital scarcity would be evident which would reduce businesses, development, livelihood, and eventually the quality of life. The need to promote and mitigate water of bodies such as bays is therefore highly important for management. Thus, policymakers and government sectors may take this into consideration for promotion and conservation of natural resources.