Over the last few decades, it has become clear that microbiota are of vital importance for the survival, homeostasis, and overall development of marine mollusks, and that shifts in their microbiota can dictate chances of survival into adulthood (McFall-Ngai et al., 2013). Rapid improvements in the technology used to assess microbial communities have led to an expansion of the breadth and scope of microbial ecology research over the past 20 years. Here, 16S rRNA gene amplicons were used to evaluate how microbial compositions shift in response to exposure of environmentally relevant concentrations of atrazine found within the Chesapeake Bay (30 µg/L, 20µg/L, 10µg/L and 3 µg/L respectively). The Chesapeake Bay has suffered a dramatic loss of its native mollusk species, the Eastern oyster (Crassostrea virginica). It is believed that this loss is caused in part by contamination of the Bay with atrazine, a herbicide that washes off of agricultural crops and penetrates into surrounding surface and groundwaters following heavy periods of rain in spring and summer months. Although, the manner in which atrazine hinders the survival of oysters remains unknown, the present study investigates how exposure of atrazine to C. virginica affects its core microbiome. The dominant bacterial groups found within all groups included those belonging to the order Rickettsiales, Vibrionales, and Alteromonadales, family Pseudoalteromonadacea, Vibrionaceaea, and Planctomycetaceae, and genus Pseudoalteromonas, Vibrio and Nocardia. Although our results confirm that oysters maintain similar core microbial communities over time, we also report a novel finding, namely, that oysters exposed to atrazine concentrations as low as 3µg/L saw a significant loss of Vibrio and Pseudoalteromonas species interactions and underwent a subsequent colonization of Nocardia species. Because the microbiome of C. virginica is vital for its homeostasis and survival, this result suggests that the presence of atrazine in the Chesapeake Bay is in part responsible for widespread decline in this species population.