Combined Sewer Overflow Control and Partnership Act of 1999 - Amends the Federal Water Pollution Control Act to require each permit, order, or decree issued under such Act for a discharge from a combined storm and sanitary sewer to conform to the Combined Sewer Overflow Control Policy signed by the Administrator of the Environmental Protection Agency on April 11, 1994. Authorizes the Administrator, notwithstanding specified compliance schedules and permit limitations, to issue or execute a permit, order, or decree for discharges from such sewers that includes a schedule for compliance with a long-term control plan for a term of up to 15 years. Provides for extensions of such term, as appropriate.

Declares that no permit, order, or decree issued under the Act should require compliance with water quality based requirements contained in a long-term control plan under the Control Policy unless the Administrator has completed the water quality standards-designated use review process called for in the Control Policy.

Authorizes the Administrator to make grants to municipalities for planning, design, and construction of facilities to intercept, transport, control, or treat combined storm and sanitary sewer flows.

Directs the Administrator to report biennially to Congress on recommended funding levels for the two fiscal years following the date of a report on activities relating to combined storm and sanitary sewer flows.

Authorizes appropriations for FY 2000 through 2004.