May aquatic and upland fish and wildlife habitat restoration and enhancement projects be constructed in wild and scenic rivers, including the placement of in-channel structures?

Yes. Such projects may be constructed to protect and enhance fish and wildlife. In-channel structures (e.g., placement of large wood to replicate natural stream conditions) and in-channel activities (e.g., dredging to protect listed species) are acceptable, provided they do not have a direct and adverse effect on the values of the river (its free-flowing condition, water quality, and outstandingly remarkable values. Similarly, in-channel habitat projects may also be constructed below/above a designated river so long as they do not unreasonably diminish the scenic, recreational, and fish and wildlife values of the wild and scenic river. 

When fish and wildlife species and/or habitat are an outstandingly remarkable value, restoration and enhancement projects may be an important component in a protection strategy. The potential effect of such project proposals on other outstandingly remarkable values, such as recreation and boating, should be carefully considered in project design.

Upland (above the river’s ordinary high water mark) habitat restoration and enhancement projects may be constructed on federal or private lands. On federal lands such activities (e.g., a wildlife guzzler) must be judged to protect or enhance river values. Such proposals on private land may be subject to local zoning.

Source
Interagency Wild & Scenic Rivers Council