A commercially available electromagnetic flowmeter is attached to a seepage cylinder to create an electromagnetic seepage meter (ESM) for automating measurement of fluxes across the sediment/water interface between ground water and surface water. The ESM is evaluated through its application at two lakes in New England, one where water seeps into the lake and one where water seeps out of the lake. The electromagnetic flowmeter replaces the seepage-meter bag and provides a continuous series of measurements from which temporal seepage processes can be investigated. It provides flow measurements over a range of three orders of magnitude, and contains no protruding components or moving parts. The ESM was used to evaluate duration of seepage disturbance following meter installation and indicated natural seepage rates resumed approximately one hour following meter insertion in a sandy lakebed. Lakebed seepage also varied considerably in response to lakebed disturbances, near-shore waves, and rainfalls, indicating hydrologic processes are occurring in shallow lakebed settings at time scales that have largely gone unobserved.