Does the Forest Service as the river-administering agency have the authority to prohibit a landowner from using bank stabilization measures?
No. The Forest Service does NOT have the authority to prohibit a landowner from using bank stabilization measures. That authority resides with the assisting federal agency, typically the ACOE through its administration (33 CFR 320) of Section 10 of the Rivers and Harbors Act and Section 404 of the Clean Water Act. The assisting federal agency may not authorize bank stabilization or other water resources projects determined by the Forest Service to adversely affect the values for which the river was established (16 USC 1278).