To establish permit requirements for overflows from combined storm water and sanitary sewer systems discharging into the estuarine zone and marine waters and to require the correction of such systems to minimize discharges into those waters, to mitigate the effects of pollution discharges into estuaries and oceans, and for other purposes.

Title I: Combined Sewer and Storm Water System Overflow Control - Estuarine Zone and Marine Waters Combined Sewer Overflow Control Act - Amends the Federal Water Pollution Control Act to require the Administrator of the Environmental Protection Agency to issue regulations setting forth permit requirements for discharges from combined storm water and sanitary sewer overflows into the estuarine zone and marine waters. Directs the Administrator, in determining the content of such regulations, to take into account; (1) the expected composition, frequency, and volume of each discharge; (2) the anticipated effect of each discharge on the environment, economy, and aesthetic and recreational values of the receiving waters; and (3) the need for a flexible approach in minimizing such discharges.

Authorizes the Administrator to issue permits after 1999 for such discharges only if the permittee has taken reasonable efforts to eliminate dry weather discharges and to minimize wet weather discharges.

Requires the Administrator to provide technical assistance to State and local governments issued permits under this Act.

Directs permittees, as a condition for permit issuance or renewal, to budget and expend an amount of funds for: (1) identifying all discharges of overflows into the estuarine zone and marine waters; (2) implementing technology-based limitations of such discharges; and (3) eliminating such discharges. Waives such requirement if the Administrator determines that the permittee or the State in which such permittee is located has begun to implement a plan that will result in the cessation of dry weather discharges and minimization of wet weather discharges by the year 2000.

Makes funds available to permittees to address water quality problems resulting from such discharges.

Directs the Administrator to report to the Congress on: (1) the feasibility and cost of establishing a technological clearinghouse to make available to States and local governments information on, and assistance in, controlling and ceasing discharges of overflows from combined storm water and sanitary sewers into the estuarine zone and marine waters; and (2) the major components of discharges which contribute significantly to floating debris and debris which washes up on shores and ways to eliminate the introduction of such debris into combined storm water and sanitary sewer systems.

Authorizes appropriations.

Title II: National Estuary Program Amendment - National Estuary Program Amendment Act - Requires the Administrator to: (1) identify estuaries where overflow discharges from combined storm water and sanitary sewer systems constitute a major source of pollution; (2) urge that the management conference for each estuary develop a priority action plan to address such overflows; and (3) report to the Congress on the extent of such discharges and the anticipated Federal cost of addressing the problem.

Title III: Marine Pollution Discharge Abatement - Marine Discharge Abatement Act - Prohibits the issuance or renewal of permits for pollutant discharges into estuaries, estuarine zones, the territorial sea, the waters of the contiguous zone, or the oceans unless: (1) the need for the discharge has been demonstrated by the applicant and the Administrator has determined there is no environmentally sound alternative; (2) the permittee establishes an on-going monitoring program for each discharge; and (3) the applicant agrees to include within the permit a provision to allow the Administrator to modify or terminate such permit if such action is in the public interest and necessary to prevent the degradation of such waters.

Directs the Administrator and the Under Secretary of Commerce for Oceans and Atmosphere to review existing guidelines and to promulgate guidelines necessary to prevent the degradation of such waters.

Prohibits the waiver of such requirements for permit issuances or renewals.