To amend the Federal Water Pollution Control Act to reauthorize the Great Lakes program, and for other purposes.

Amends provisions of the Federal Water Pollution Control Act regarding the Great Lakes to authorize the Administrator of the Environmental Protection Agency to make grants to States, Indian tribes, interstate agencies, and local governments for projects to improve water quality at areas of concern. Limits the Federal share of project costs to 60 percent. Authorizes appropriations.

Permits the Administrator to undertake projects to improve degraded fresh water estuary habitat (with respect to bodies of water having unimpaired natural connections with a Great Lake and within which the water from the Great Lake is measurably diluted with water from land drainage) for purposes of attaining self-sustaining systems integrated into the surrounding landscape. Limits the Federal share of project costs to 65 percent.

Reauthorizes the Great Lakes program for FY 2001 through 2005.