Combined Sewer Overflow Control and Partnership Act of 1998

Combined Sewer Overflow Control and Partnership Act of 1998 - Amends the Federal Water Pollution Control Act to require each permit, order, or decree issued pursuant to 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.

Modifies any administrative or judicial decree or order issued before this Act's enactment date that establishes any deadline or schedule for the construction of treatment works for control of any discharge from a municipal combined sewer system to extend such deadlines or schedules to conform with this Act, at the request of the municipal owner or operator.

Prohibits any permit, order, or decree issued pursuant to the Act from requiring 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.

Authorizes appropriations for FY 1999 through 2001.

Directs the Administrator to report biennially to the 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.