Clean Water Infrastructure Financing Act of 1999

Clean Water Infrastructure Financing Act of 1999 - Amends the Federal Water Pollution Control Act to provide that capitalization grants to States for the establishment of water pollution control revolving funds (revolving funds) shall be for providing assistance to accomplish the purposes of such Act. (Currently, such grants are provided for assistance for specific purposes.)

Removes certain requirements for States with respect to construction of treatment works under capitalization grant agreements.

Directs the Administrator of the Environmental Protection Agency to assist States in establishing simplified procedures for small water systems to obtain assistance under the Act.

Requires revolving funds to be used only for providing assistance for activities that have as a principal benefit the improvement or protection of water quality of navigable waters. Adds activities to the list of those which may be assisted.

Provides for a repayment period of the lesser of 40 years or the expected life of the project to be financed with loan proceeds with respect to loans made to disadvantaged communities from revolving funds. Requires loans made from such funds to be fully amortized upon the expiration of the loan term (currently, no later than 20 years after project completion). Requires such funds to provide: (1) loan guarantees for developing and implementing innovative technologies; and (2) technical, planning, and other specified assistance to small systems.

Treats a treatment works as a publicly owned treatment works, for purposes of eligibility for construction assistance from a revolving fund, if the treatment works, without regard to ownership, would be considered a publicly owned treatment works and is principally treating municipal waste water or domestic sewage.

Provides for negative interest rates of up to two percent to reduce the unpaid principal on loans from revolving funds made to disadvantaged communities.

Reauthorizes appropriations for FY 2001 through 2005 for the revolving fund program.