Short Sea Shipping Act of 2009 - Amends the Internal Revenue Code to exempt from the harbor maintenance tax commercial cargo (other than bulk cargo) loaded at: (1) a port in the U.S. mainland and unloaded at another such port after transport solely by coastal route or river or unloaded at a port in Canada located in the Great Lakes Saint Lawrence Seaway System; or (2) such a port in Canada and unloaded at a port in the U.S. mainland.
Defines the "Great Lakes Saint Lawrence Seaway System" as the waterway between Duluth, Minnesota, and Nova Scotia, encompassing the five Great Lakes, their connecting channels, and the Saint Lawrence River.