Great Lakes Ecology Protection Act of 2003 - Amends the Nonindigenous Aquatic Nuisance Prevention and Control Act of 1990 to direct the Secretary of Transportation to issue regulations to: (1) prevent the introduction and spread of aquatic nuisance species within the Great Lakes; and (2) among other things require the use of environmentally sound treatment methods for ballast water and ballast sediments in preventing and controlling infestations of such species.Requires the Secretary to maximize public participation in proposed rulemaking with respect to such regulations.
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