Great Lakes Water Protection Act of 2003 - Amends the Nonindigenous Aquatic Nuisance Prevention and Control Act of 1990 to direct the Secretary of the department in which the Coast Guard is operating to issue, within 30 days after enactment of this Act, a regulation that prohibits any vessel with a ballast water tank from entering the Great Lakes if more than five percent of the capacity of the tank contains ballast water.
Requires the master of such a vessel to certify compliance with such prohibition to the Secretary or the Secretary's designee before the vessel's departure from the first lock in the St. Lawrence Seaway.