Oyster (Crassostrea virginica) aquaculture has a long history and tradition in Long Island Sound (Connecticut, USA). Although most of the producers practice traditional on-bottom aquaculture, there are a growing number of individuals utilizing bottom gear for cultivation and depuration. The use of this gear presents a potential conflict in eastern Long Island Sound where the last remaining populations of eelgrass (Zostera marina L.) exist. Shellfish aquaculture activity has been identified as a potential source for negative impacts to eelgrass populations. However, bivalve aquaculture has also been shown to provide an equivalent or greater degree of ecosystem services as submerged aquatic vegetation. The effects of short-term oyster depuration activity were gauged by comparing eelgrass reference sites and experimental plots (eelgrass areas containing oyster depuration cages with and without oysters) in triplicate. Changes in sheath length of the eelgrass 1 m from the cages were used as a proxy for growth rate. The aquaculture gear had no effect on this measure of growth rate of eelgrass in any of the deployments. Sediment characteristics (sediment chlorophyll, sediment % organics) in the cage footprint and 1m from the cages also failed to show an effect of the depuration cages on the local environment. Video monitoring of the footprints and local area indicated little physical damage to the eelgrass beds as a result of the short deployment of the aquaculture gear. The water column at all three sites was vertically well mixed and no effect of the cages on water column light and other characteristics was detectable. The results of this study indicated that at the current level of activity, short-term depuration of oysters has minimal effect on eelgrass growth, water quality and the sediment characteristics measured. However, if depuration activity expands in terms of the amount of gear and/or individual operations, it may result in measurable effects. Understanding the interactions between shellfish aquaculture activity and the marine environment is necessary for sustainable growth of the industry.