Great Lakes Short Sea Shipping Enhancement Act of 2011 - Amends the Internal Revenue Code to exempt from the harbor maintenance tax commercial cargo (other than bulk cargo) loaded or unloaded at U.S. ports in the Great Lakes Saint Lawrence Seaway System. Defines the "Great Lakes Saint Lawrence Seaway System" as the waterway between Duluth, Minnesota, and Sept Iles, Quebec, Canada, encompassing the five Great Lakes, their connecting channels, and the Saint Lawrence River.