The presence of bacterial pathogens in bivalve shellfish harvested from the marine ecosystem globally has continued to raise serious food safety concerns, thereby undermining the nutritional and health benefits derived from their consumption. Four species of bivalve shellfish: Bloody cockle (Anadara senilis), Donax clam (Donax rugosus), Knife clam (Tagelus adansonaii) and Mangrove oyster (Crassosstra gasar) harvested from the brackish waters of the Niger Delta were assessed for their bacterial pathogens. Standard methods of analysis were employed to assess microbiological hazards accumulated by shellfish species. The results of the microbiological analysis revealed that the total viable count (TVC) was lower than the recommended limit (5.7 log cfu/g) for fresh bivalve shellfish while Vibrio cholerae, Vibrio parahaemolyticus, Salmonellaspp, Shigellaspp, Listeria monocytogenes and E. coli were far above the stipulated FDA standard for molluscian shellfish. The loads of microbiological hazards in bivalve species indicated that in all the locations, Bloody cockle and Donax clam accumulated more bacterial pathogens while the samples harvested from Ibeno and Iko Town brackish waters were lower in pathogenic loads when compared to shellfish harvested from Andoni and Bonny location. The result obtained in this study is of public health importance since, it will serve as a guide towards improved processing techniques and stimulate actions towards the development of novel surveillance as well as, prevention and control strategies, that will help to reduce foodborne disease outbreaks associated with shellfish.