Fish normally accumulates heavy metals from food, water and sediments which can be harmful to human health. In the present study, levels of Pb, Hg and Cd; relationships with size; and seasonal variation in six aquaculture commodities mud crab, Scylla serrata; milkfish, Chanos chanos; green mussel, Perna viridis; oyster, Crassostrea iridalei; shrimp, Penaeus spp.; and tilapia, Oreochromis niloticus from Manila Bay fish landing sites were determined. Homogenized flesh samples were subjected to microwave-assisted digestion in a mixed solution of nitric acid and hydrogen peroxide before analysis by Atomic Absorption Spectrophotometer. All commodities passed the regulatory limit set by Bureau of Fisheries and Aquatic Resources Fisheries Administrative Order 210s 2001 and European Commission 1881/2006 for Pb and Cd. In contrary, 2.04% O. niloticus from Hagonoy, Bulacan and Navotas City and 5.00% Penaeus spp. from Guagua, Pampanga and Obando, Bulacan exceeded the limit for Hg. Significant negative relationships were found between Cd concentration and fish size in C. chanos and P. viridis, while significant positive correlations were observed between Pb and fish length in O. niloticus and S. serrata; Hg and fish length in P. viridis; and Cd and fish weight in Penaeus spp. Aquaculture commodities were observed to have significantly higher level of accumulation during wet season. Results indicate that metal concentration varies among aquaculture commodities, landing sites and season of catch. Thus, there is a need for risk assessment and regular monitoring for the said commodities.