Food poisoning is caused by pathogenic bacteria in water and aquatic products, especially bivalves (e.g., oysters, clams), which can bioaccumulate pathogenic bacteria. Polluted water and aquatic products thus pose a serious threat to human health and safety. In this study, the types of pathogenic bacteria in water samples and shellfish collected from the Dadeng offshore area in Xiamen were examined. We also analyzed the relationships between dominant pathogens and major climate and water quality parameters. Our objective was to provide reference data that may be used to help prevent bacterial infections and to improve aquatic food hygiene in Xiamen and its surrounding areas to safe levels, thus ensuring the health of Xiamen residents. We found that the main pathogenic bacteria were Vibrio and Bacillus, with the dominant pathogen being Vibrio parahaemolyticus. Physical and chemical indexes (water temperature, salinity, pH, dissolved oxygen, and turbidity) of water bodies and the 3-day accumulated rainfall were found to be important factors affecting the occurrence and abundance of V. parahaemolyticus.