Federal Facilities Clean Water Compliance Act of 1999

Federal Facilities Clean Water Compliance Act of 1999 - Amends the Federal Water Pollution Control Act (the Act) to require each Federal department, agency, and instrumentality to be subject to and comply with all Federal, State, and local requirements with respect to the control and abatement of water pollution and management in the same manner and extent as any person is subject to such requirements, including the payment of reasonable service charges. Waives immunity of the United States with respect to any such requirements.

Absolves Federal employees of personal liability for civil penalties under water pollution control laws for acts or omissions within the scope of official duties. Makes Federal employees subject to criminal sanctions under Federal or State water pollution laws, but prohibits applying criminal sanctions to Federal agencies.

Authorizes the Administrator of the Environmental Protection Agency, the Secretary of the Army, and the Secretary of the department in which the Coast Guard is operating to pursue enforcement actions under this Act. Requires States to use funds collected from the Federal Government under this Act only for projects designed to improve or protect the environment or to defray the costs of environmental protection or enforcement.

Includes Federal agencies within the definition of "person" for purposes of the Act.