The physical parameters of seawater are important determinants of water quality. Heavy metals are components that are naturally present in a considerable amount in the ocean but are observed to be rising above the allowable level due to pollution outputs of industrialization. Heavy metal contamination is among the environmental pollution problems that the world faces. Additionally, hydrogen sulfide (H2S) is also a toxic compound that accumulates in the ocean floor posing threat to the marine organisms when present in high concentrations. The objective of this study is to document the distribution of temperature and salinity in the water column, heavy metals (Pb, Cd, Hg) and sediment H2S in Manila Bay from 2012 to 2015. Stratification in the bay was generally a factor of salinity and less of temperature. Stratification due to salinity was consistently observed in September with the halocline occurring around 10 m to 15 m. Most of the time, the bay had evenly distributed temperatures, but the slightly higher temperatures were usually recorded near the coast. Inverse trends were observed for the salinity and temperature of the bay. Pb, Cd, and Hg concentrations in the bay occasionally exceeded the permissible limits especially the lead concentration in January 2013 (ave: 809.81 µg/L), March 2013 (ave: 1102.88 µg/L) and November 2015 (1507.50 µg/L). Cd and Hg concentrations were generally below the permissible limit and the reported limit of analysis. H2S concentration ranged from < 4 mg/kg to 9.99 mg/kg for all the survey months. Distribution was higher in the northwestern part and southeastern areas of the bay.