Coastal pollution is of public health concern due to the possibility of bacterial contamination in aquaculture affecting health risk and seafood safety. This study determined the concentrations of total coliforms, fecal coliforms, E. coli, and V. parahaemolyticus and the presence of V. cholerae and Salmonella in water and measured water quality and meteorological factors from the major oyster cultivation areas in Thailand. The water samples (n = 363) were collected from Surat Thani (n = 60), Chanthaburi (n = 60), Trat (n = 60), Phetchaburi (n = 60), Chonburi (n = 63), and Phang Nga (n = 60) from February 2021 to January 2022. The prevalence of total coliforms (96.7%), fecal coliforms (60.6%), E. coli (22.9%), along with the prevalence of Salmonella (2.5%), Vibrio parahaemolyticus (74.9%), and V. cholerae (11.3%) were determined. Common Salmonella serovars were Othmarschen and Lamberhurst. The concentration of E. coli was significantly associated with dissolved oxygen and precipitation (p < 0.0001). Therefore, continuing microbiological monitoring and surveillance of water for coastal aquaculture is important to produce safe aquatic products. Furthermore, raising awareness of coastal pollution and seafood safety will help enhance sustainable coastal fisheries in Thailand.