Sea lamprey (Petromyzon marinus) control is achieved in the Laurentian Great Lakes by applying lamprey-specific pesticides (lampricides) to habitats containing larval sea lamprey. Lampricide treatments cost less and are more effective in watersheds where dams block adult sea lamprey migration and limit larval distribution relative to watersheds with no barriers to migration. However, dams impound water and can block movement of valued fishes, outcomes that are untenable for some stakeholders. Here, a seasonal and non-physical barrier of pulsed direct electrical current was tested to block adult sea lamprey while also monitoring the movement and mortality of non-target fish species. The electric barrier was operated in the Black Mallard River, a tributary to northern Lake Huron, March through August 2016–2018. The electric field blocked adult sea lamprey; 1056 adult sea lamprey were captured downstream of the electric field and two were captured upstream of the electric barrier over the three-year study. In 2018, larval sea lamprey abundance upstream of the barrier was about 50% less than historical averages, and genetic analysis found that roughly 98% of larvae upstream of the barrier were spawned in years prior to barrier installation. When the barrier was electrified, non-target fish species were blocked, and a small percentage (<3%) were killed. This study demonstrated that a seasonally deployed electric barrier can reduce the abundance of larval sea lamprey upstream without impounding water, but effects on the movements and survival of other fish species remain a concern.