The coliform group of bacteria is widely used as an indicator of pollution related to the presence of pathogenic bacteria linked to fecal contamination, which poses great health risk. This study aimed to establish baseline information on the coliform contamination in water and fishery resources in Manila Bay aquaculture farms. Water samples and major aquaculture commodities were collected twice per season from representative aquafarms in the coastal provinces of the bay and were analyzed for total coliform (TC), fecal coliform (FC), and E. coli (EC) using the Multiple Tube Fermentation method of the Bacteriological Analytical Manual. TC, FC, and EC in water were found higher during the wet season, their average concentrations being 8,747, 2,808, and 1, 216 MPN/100mL, respectively; while those in the dry being 6,255, 1,223, and 286 MPN/100mL, respectively. More samples exceeded the DENR Standard Limit for TC (5,000 MPN/100mL) in the wet season than in the dry season (roughly 25% vs 10%). Farmed fishery resources, on the other hand, had higher EC concentrations during the dry season. The following are the percentages of samples that exceeded DENR Standards: 25% of mussels, 24.44% of shrimps, 16% of tilapia, 14.67% of oysters, 8.89% of crabs, and 6.67% of milkfish.