Biscayne Bay is a shallow oligotrophic estuary in Southeast Florida. Channelization of rivers, and dredging of canals has greatly altered the historical flow of fresh water into the bay. This, coupled with the rise of a sprawling urban & suburban development, has greatly increased the nutrient load in the bay. This study examined the bacterial community at 14 stations throughout Biscayne Bay —6 stations were located at the mouths of canals; 1 upstream-canal station; 6 stations in the center of the bay; and one ocean influenced station, located near the entrance to the bay. One liter, surface water samples were taken monthly for one year. The 16S rRNA gene was used to identify bacterial community composition. There were 19,680 Amplicon Sequence Variants (ASVs) identified across all 146 samples. Salinity and total phosphorous were the primary factors explaining bacterial biodiversity. Biodiversity in microbial communities in the Miami River and the ocean influenced site, were unique compared to other sites in the study. Alpha and β-diversity were generally homogeneous over most of the study area. Looking at α- diversity, the two stations on the Miami River were statistically identical and had higher diversity. The ocean influenced station, located near the Safety Valve, was statistically unique, and had lower α-diversity. The remaining 11 stations had moderate diversity and were statistically identical, appearing to be a combination of the previously mentioned Miami River sites and the ocean influenced site. Beta diversity showed a similar pattern; with the exception that the site located at the mouth of Black Creek could now be grouped with the Miami River sites.