Oysters in coastal and estuarine environments are subject to fluctuating environmental conditions, including nutrient loading, runoff, pollution, and anoxia, that may impact their health and the ecosystem services they provide. We propose that these variations in environmental conditions cause changes in their associated microbial community structure and function. Adult wild oyster gut and seawater samples were collected at 5 sites along an estuarine nutrient gradient in Narragansett Bay, Rhode Island, USA in August 2017. Samples were analyzed by 16S rRNA sequencing of the V6 region to characterize bacterial community structures and metatranscriptomes were sequenced to determine oyster gut microbial function.