In the 1993 case PUD No. 1 of Jefferson County and City of Tacoma v. Washington Department of Ecology, et al., the U.S Supreme Court ruled in favor of the Washington State Department of Ecology, upholding its authority to impose conditions on a hydroelectric project for certification under Section 401(a) (1)of Clean Water Act. The Public Utility District No. 1 (PUD) had sought to construct a hydroelectric power plant and applied for water quality certification from the state department, which was granted with certain conditions including maintaining minimum stream flows to protect fishery resources downstream from the proposed project site. PUD challenged these conditions arguing that they were beyond what is allowed by federal law under section 401(a)(1). However, Supreme Court held that states have broad authority under this provision not only to enforce their own water quality standards but also other appropriate requirements related to protection and preservation of aquatic life.

In the dissenting opinion for PUD No. 1 of Jefferson County and City of Tacoma v. Washington Department of Ecology, Justice Thomas argued that the majority's interpretation was an overreach in federal power under the Clean Water Act (CWA). He contended that Section 401(d) should not be interpreted to allow states to impose conditions unrelated to water quality on a federally licensed project. Instead, he believed it only allowed states to enforce compliance with state laws relating directly to water pollution control or prevention measures. The broad interpretation by the majority would give states veto power over federal projects, which could lead them into areas traditionally reserved for federal regulation such as energy production and transmission facilities licensing - something Congress did not intend when drafting CWA.