West Falmouth Harbor, a shallow lagoon on Cape Cod, has experienced a threefold increase in nitrogen load since the mid- to late 1990s due to input from a groundwater plume contaminated by a municipal wastewater treatment plant. We measured the exchange of nitrogen and phosphorus between the harbor and the coastal waters of Buzzards Bay over several years when the harbor was experiencing this elevated nitrogen load. During summer months, the harbor not only retained the entire watershed nitrogen load but also had a net import of nitrogen from Buzzards Bay. During the spring and fall, the harbor had a net export of nitrogen to Buzzards Bay. We did not measure the export in winter, but assuming the winter net export was less than 112 % of the load, the harbor exported less than half of the watershed nitrogen load on an annual basis. For phosphorus, the harbor had a net import from coastal waters in the spring and summer months and a net export in the fall. Despite the large increase in nitrogen load to the harbor, the summertime import of phosphorus from Buzzards Bay was sufficient to maintain nitrogen limitation of primary productivity during the summer. Our findings illustrate that shallow systems dominated by benthic producers have the potential to retain large terrestrial nitrogen loads when there is sufficient supply of phosphorus from exchange with coastal waters.