Riparian vegetation includes black cottonwood (Populus trichocarpa), bulrush (Scirpus spp.), and cattails (Typha spp.). Willows (Salix spp.) are most common in the vicinity of the dam and the falls to the north and south of the Monument.
There are locally dense stands of the invasive Russian olive (Eleagnus angustifolia) along the shore, and purple loosestrife (Lythrum salicaria) and saltcedar (Tamarix spp.) are also invading.
Other aquatic vegetation includes coontail (Ceratophyllum demersum), duckweed (Lemna spp.), watercress (Rorippa nasturtium-aquaticum), and pondweed (Potamogeton spp.). Algal mats commonly form on the surface of the Snake River in warm weather.
The Monument is also important to microbiotic plants, usually forming a soil crust or found on aging brush or rocks. USGS-BRD botanists have indicated that the exclusion of grazing makes portions of the Monument significant as a botanical preserve.
Facilitating the conservation of Idaho's biological diversity, the Idaho Conservation Data Center maintains a list of plant and animal species of special concern. Three such plant species, whose sites need protection, are known to occur in the Monument: the giant helleborine (Epipactis gigantea), the cowpie buckwheat (Eriogonum shockleyi var. shockleyi), and the Owyhee mourning milkvetch (Astragalus atratus var. owyheensis).