The proposed introduction of Crassostrea ariakensis along the mid-Atlantic Coast of the United States has sparked controversy regarding ecological, economic, and human health consequences. Previous research has focused primarily on the ecological and socioeconomic implications of this initiative, yet few studies have assessed the potential impacts on public health. This study compares rates of bioaccumulation, depuration, and post-harvest decay of Escherichia coli and Vibrio sp. between Crassostrea virginica and C. ariakensis. Our results suggest that (1) bioaccumulation rates of E. coli in C. ariakensis were significantly lower than those for C. virginica, (2) depuration of E. coli was variable between the two species, and (3) C. ariakensis post-harvest decay rates of E. coli were significantly lower than in C. virginica. This research provides a first comparison between C. ariakensis and C. virginica with regards to bacterial dynamics, an important consideration when determining appropriate shellfish management strategies.