Mitigating coastal eutrophication is a global challenge. In many places where land-based management has reduced nutrient discharges, coastal waterbodies remain impaired. This study examined ‘bioextraction’ of nutrients from the water by oyster aquaculture in Long Island Sound, Connecticut, as an example of how aquaculture might complement land-based measures in urban estuaries. Eutrophication status, nutrient removal, and ecosystem service value were estimated through eutrophication assessment, application of hydrologic, circulation, and local- and ecosystem-scale models, and economic valuation. System-scale modeling estimated that current oyster aquaculture, via sequestration into tissue and shell only, removes an equivalent of 1.31%, and expanded production could remove 2.68%, of total annual land-based nitrogen inputs by aquaculture alone. Up-scaled local-scale results were similar to results from the system-scale modeling, suggesting that this upscaling method could be useful in waterbodies without circulation models. The minimum value of the ecosystem service of nitrogen removed by oyster production was estimated by means of an avoided costs method, which uses the cost of alternative nutrient management measures such as wastewater treatement and urban Best Management Practices to estimate the value of the removed nitrogen, to be $8.5 million per year, with maximum value at expanded production of $470 million per year. Removal and value estimates are conservative because they do not include removal by clams in Connecticut due to the lack of a clam model, or by oysters and clams in New York due to data limitations, nor denitrification losses. If oyster associated removal from all Connecticut and New York lease acres (5% of bottom area) and denitrification losses for both states are included, nitrogen removal estimates increase to 10% – 30% of total annual inputs. The total N removal could be higher if removal by clams is included. Additional research is needed for inclusion of shellfish growers in nutrient trading programs. These optimistic results are specific to Long Island Sound but the modeling approach is transferable and can be used to evaluate possible contribution by shellfish aquaculture in other urban estuaries.