Heavy metals (HM) are high-atomic weight elements hazardous at very low concentrations. Despite the health risk HM contamination brings, studies conducted were only confined to the offshore and marine portions of the bay. Hence, this study was conducted to establish baseline information and compare the spatial and seasonal distribution of heavy metal contamination in water and fishery resources in aquaculture farms and coastal areas in Manila Bay. Water and major aquaculture commodities were collected in November 2014, February 2015 and April 2015 and were analyzed for lead (Pb), cadmium (Cd), and mercury (Hg) using the following methods: (1) Graphite Furnace Atomizer-Atomic Absorption Spectrophotometry (GFA-AAS) for Pb and Cd and (2) Mercury Vaporizing Unit-AAS (MVU-AAS) for Hg. Cd (Bataan, Cavite, Bulacan, and Pampanga) and Hg (Cavite and Pampanga) in water were found significantly higher during the dry season (p < 0.05). In contrast, Pb in water was relatively higher during the wet season but levels were not significantly different with those in the dry. Several sites in Bataan, Bulacan, and Cavite, exceeded DENR regulatory limits for Pb and Hg in water by 1.35 to 1.8%. As for the fishery commodities, 2/12 milkfish samples and 1/9 exceeded regulatory limit for Pb in finfish (0.3 mg/kg) by 1.03 to 3.57% while 1/12 milkfish samples and 1/13 oyster samples exceeded the limit for Hg in bivalves (0.5 mg/kg) by 0.45 to 0.75%.