Manila Bay is surrounded by industrial, urban and populated cities of the Philippines and exposed to various pollutants. A hydrodynamic model previously simulated with the influence of tides, winds, rivers and pharmaceutical pollutants showed high dissolved organic pollutant concentration near Pasig & Pampanga Rivers and on the eastern side of the bay where mariculture, especially mussels proliferate (Enova et al, in progress). These organic pollutants may contribute to lower dissolved oxygen (DO) and hypoxic conditions (<2 mg/L) deeper than 4 m in Navotas, and 6 meters in Paranaque. Low DO levels at the bottom waters are consistent with anecdotal reports from fisherfolks that mussels survive at the upper 2 meters of the water column in the past few years rather than at the seafloor. Monitoring of dissolved oxygen is vital in this area as it may affect mussel growth and reproduction. Moreover, targeted monitoring and analysis of specific organic pollutants and other factors that may contribute to hypoxia is recommended for a more comprehensive discussion of the health of Manila Bay and sustainability of mariculture.