In the case of S. D. Warren Company v. Maine Board of Environmental Protection, the Supreme Court ruled in favor of Maine's environmental regulators, affirming that states have authority under the Clean Water Act to impose conditions on hydropower projects even if they are federally licensed. The dispute arose when S.D. Warren Co., a paper manufacturer operating five dams on a river in Maine, argued that its dams did not result in discharge into navigable waters and thus should be exempt from state certification requirements under Section 401 of the Clean Water Act (CWA). However, both lower courts and ultimately the Supreme Court disagreed with this argument stating that dam operations do cause changes to water quality which falls within jurisdictional boundaries set by CWA for state regulation.

In the S. D. Warren Company v. Maine Board of Environmental Protection case, there was no dissenting opinion recorded as it was a unanimous decision by the Supreme Court justices in favor of the Maine Board of Environmental Protection et al., 2006. The court ruled that dams operated by paper mills on rivers in Maine were subject to federal licensing requirements under section 401 of the Clean Water Act because they cause changes in water flow and temperature which constitute "discharge" into U.S waters, thus requiring certification from state authorities for compliance with environmental standards before obtaining or renewing licenses from Federal Energy Regulatory Commission (FERC).