Federal Wetlands Jurisdiction Act of 2004

Federal Wetlands Jurisdiction Act of 2004 - Amends the Federal Water Pollution Control Act (FWPCA) to clarify that waters of the United States, including the territorial seas, are subject to the jurisdiction of the permitting program for the discharge of dredged or fill material if such waters are: (1) navigable; (2) hydrologically connected to navigable waters through a continuous, naturally occurring surface connection; or (3) wetlands adjacent to such navigable or hydrologically connected waters.

States that waters are considered hydrologically connected to navigable waters for purposes of this Act if connected by perennial or intermittent streams that contribute flow to navigable waters. Excludes from the definition those waters connected by: (1) sheet flow; (2) ephemeral waters, ground water, manmade ditches, or pipelines; or (3) a municipal separate storm sewer system or any other regulated point source.

Excludes fastlands (areas located behind legally constituted manmade structures) from the jurisdiction of the permitting program for the discharge of dredged or fill material.

Sets forth procedures whereby property owners, or those with written authorization from such owners, may: (1) request that the Secretary of the Army determine jurisdiction under this Act and thereafter seek judicial review or injunctive relief; or (2) proceed under the administrative appeals process.

Transfers to the Secretary of the Army, acting through the Chief of Engineers, the Environmental Protection Agency (EPA) Administrator's authority over permits for the discharge of dredged or fill material into navigable waters under the FWPCA. Allows the Administrator to retain authority to comment on such permits.