Federal Facilities Clean Water Compliance Act of 1999

Federal Facilities Clean Water Compliance Act of 1999 - Amends the Federal Water Pollution Control Act to waive immunity of the United States with respect to Federal, State, interstate, and local requirements pertaining to water pollution control, including requirements for permits or reporting, injunctive relief, sanctions to enforce relief, payment of reasonable service charges, administrative orders, and penalties or fines.

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 control 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 against Federal agencies under the Act.

Requires States, unless a State law or constitution requires otherwise, to use penalties collected from the Federal Government under the Act only for projects 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.

Authorizes citizen lawsuits for the collection by the Government of a penalty against a Federal agency assessed by the Administrator under the Act. Revises notice requirements to allow an action for a violation of standards of performance or toxic pollutant standards provisions to be brought immediately after giving notice.