The dominant vegetation type is moist evergreen lowland tropical rainforest, an eastern extension of the vast Congo Basin. It contains over 200 recorded tree species, many of which are non-native to Uganda’s central and southern forests.
Key botanical components include Cynometra alexandri, Lovoa trichilioides, Pseudospondias microcarpa, and Funtumia elastica. The canopy structure reaches 30 to 45 metres in height, with emergent trees scattered irregularly.
In poorly drained sections, especially near the river and hot springs, forest gives way to palm-dominated swamps (notably Raphia farinifera), papyrus marshes, and aquatic sedge meadows. Seasonal grasslands appear along old flood channels and trail margins.
The valley contains transitional forest–savannah ecotones, especially near Toro–Semuliki Wildlife Reserve. These ecotones support a different fauna than the park’s forest interior.