The flow of groundwater beneath barrier islands has been cited as a possible pathway for salt water and chemical exchange between a protected embayment and the open sea. Evidence is presented that identifies an exchange of groundwater through a highly permeable paleoinlet along the barrier beach of Cavallino, which separates the northern Venice Lagoon from the Adriatic Sea. We utilized both point measurements of submarine groundwater discharge (SGD) and a geophysical investigation of the subsurface resistivity to analyze the movement of saline groundwater. Discharge of groundwater and associated nutrients, was higher at the site of a former inlet than at a similar site along the barrier and modulated by the difference in tidal water level between the lagoon and Adriatic Sea. If the measured conditions are typical, storm surge barriers could potentially result in a saline groundwater flow of up to 1.5×106 m3 d−1 into the lagoon.