To understand Manila Bay’s current condition, physicochemical parameters were correlated with net phytoplankton composition from 2012 to 2015. Nitrate concentrations reached 24.18 µM, which is above the critical value (5 µM) recommended by the Philippine Department of Environment and Natural Resources and ASEAN. Hypoxia has been observed with dissolved oxygen levels as low as 1.47 mg L-1. Phytoplankton composition varies but dominated by Chaetoceros curvisetus, Skeletonema costatum, Thalassiosira sp., and Thalassionema nitzchiodes. Phytoplankton densities also vary between seasons but mostly concentrated in stations near the tributaries and urban areas. Trends in both phytoplankton and physicochemical properties suggest that the ecosystem of the bay is highly dependent on rainfall. Shannon-Wiener diversity index does not go higher than 2.46 and based on monthly averages, the bay can be categorized as moderately heavy to heavy polluted. A watershed system approach is urgently needed since found heavy eutrophication generally occurs in estuaries near urban and industrial areas.