Have other federal agencies been delegated authority to regulate activities on wild and scenic rivers?

Yes. There are four other principal agencies with authority on rivers, including wild and scenic rivers, in the United States. The EPA has authority to protect water quality; the Army Corps of Engineers (ACOE) has jurisdiction for water resources projects; the U.S. Coast Guard (USCG) has jurisdiction on inland navigable waters, vessel inspecting and licensing, safety and boating enforcement, aids to navigation, and permitting of bridges; and the Federal Energy Regulatory Commission (FERC) has authority to license the construction of hydroelectric projects.

Source
Interagency Wild & Scenic Rivers Council