Shellfish aquaculture has carbon-sequestering properties, provides nutrient stabilization, and aids in coastal protection and resilience. All these aspects are becoming increasingly important as our oceans are experiencing rising temperatures, a decrease in pH and a reduction in biodiversity. The goal of this research is to quantify the impact of shellfish aquaculture on local biodiversity and water quality at Cottage City Oysters’ commercial eastern oyster (Crassostrea virginica) farm located off the coast of in Martha’s Vineyard MA. Biodiversity was measured via environmental DNA (eDNA) metabarcoding complemented by visual surveys including GoPro video footage of larger organisms and zooplankton tows of smaller organisms. Seawater samples for eDNA metabarcoding, GoPro video footage and zooplankton tows were collected monthly from March 2022 through November 2023 from the commercial shellfish farm as well as a reference site, which contained no aquaculture equipment and had no known history of aquaculture. Water quality parameters, including seawater temperature, dissolved oxygen, pH, salinity and turbidity, were measured in the commercial farm and the reference site using a continuously monitoring Eureka multi-probe from March 2022 to November 2023. Biodiversity of organisms identified through eDNA metabarcoding, video footage and zooplankton images was quantified using the Shannon-Wiener Diversity Index. Biodiversity was highest in early autumn and lowest in early spring, demonstrating a seasonal trend following productivity trends expected for the region. The shellfish aquaculture farm also had consistently greater biodiversity than the reference site, indicating the increase of local biodiversity with the presence of shellfish farming equipment. Through the utilization of environmental DNA metabarcoding, visual surveys and long-term water quality data, this research can be used to inform resource management and policy decisions surrounding the placement of shellfish farms as a coastal resilience strategy.