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Oyster aquaculture is one of several methods for the restoration of Delaware Inland Bays; however, little is known about its potential impacts on the benthic community of the bays. In this study, water quality parameters were measured and polychaetes were collected from 24 sampling locations at Rehoboth, Indian River, and Little Assawoman Bays from July to October 2016 and 2017. We aimed to assess the impact of Eastern oyster farming under different stocking densities (50 and 250 oysters/gear) and distances away from the sites where the off-bottom gears are implemented (under gears, one meter, and five meters away). No significant impact was detected on polychaetes’ abundance and richness in regard to the presence of oyster gears. The number of polychaetes and species richness was significantly higher in Little Assawoman Bay in comparison to the Indian River and Rehoboth Bays. Results showed that the Ulva lactuca bloom that happened in 2016 could negatively impact the low abundance and richness observed in the polychaetes community. Similarly, the values of polychaetes abundance and species richness did not change significantly in samples that were taken far from the oyster gears. Dominant polychaetes families were Capitellidae and Glyceridae contributing to more than 70% of polychaetes’ number of individuals. Our results help to understand the role of oyster aquaculture in restoring the viability in the natural habitat of the Delaware Inland Bays.