An autonomous aquatic vehicle with one or more fuel cells, a controller, a plurality of sensors, a battery, and at least one electric motor and propeller. The one or more fuel cells provide power to the battery, and the battery provides power for the vehicle. Seawater is provided to anodes of the fuel cell and air or oxygen is provided to the cathode to produce power for supply to the battery. The seawater-anode reaction creates waste or byproduct that tends to decrease output of the fuel cell. The waste or byproduct is automatically flushed from the fuel cell using seawater.