Are other federal agencies responsible to protect values of rivers included in the National Wild & Scenic Rivers System?

Yes. The Wild & Scenic Rivers Act directs other federal agencies to protect river values. It explicitly recognizes the regulatory roles of the Federal Energy Regulatory Commission and the Environmental Protection Agency in protecting wild and scenic rivers, and directs other federal departments and agencies that permit or assist in the construction of water resources projects to do likewise. The role of such federal agencies in water resources project construction may be through regulation, direct funding, or indirectly funding by providing federal assistance to others.

All federal agencies that manage lands within or along wild and scenic rivers and congressionally authorized study rivers are directed to “take such action . . . as may be necessary to protect such rivers in accordance with the purposes of this Wild & Scenic Rivers Act (Section 12(a)). Please refer to the Council’s, Authorities and Roles of Key Federal Agencies (1999) for a detailed description of the authorities and roles of key federal agencies.

Source
Interagency Wild & Scenic Rivers Council