Great Lakes Controlled Data Collection and Monitoring Act - Amends the Federal Water Pollution Control Act to direct the Administrator of the Environmental Protection Agency (EPA), in cooperation with Canada and appropriate Federal agencies, to develop and implement a set of science-based indicators of water quality and related environmental factors in the Great Lakes, including measures of accumulated toxic pollutants. Directs the Administrator to establish a Federal network for regular monitoring and data collection with respect to such indicators. Requires biennial reporting of results and identification of any emerging problems.