Essential Waterways Operations and Maintenance Act of 2004 - Makes available for each fiscal year to the Secretary of the Army, acting through the Chief of Engineers, for operations and maintenance of essential waterways (in addition to amounts otherwise made available for operations and maintenance), five percent of the amount of duties collected during the preceding fiscal year on articles transported by vessel unladen for purposes of entering the customs territory of the United States.
Defines an "essential waterway" as a waterway that: (1) the Secretary of the Army determines provides service to one of the 25 highest ranked U.S. ports in terms of total tonnage of cargo transported through the port; (2) the Secretary of Energy determines is a critical component of the U.S. energy infrastructure; (3) the Secretary of Homeland Security determines provides service to at least one militarily and economically strategic port; or (4) the Secretary of Transportation determines provides service to at least one commercially strategic port.