The prairie is not known for its abundance of trees, but with over 200 acres of wetlands, cottonwoods grow well at Agate. There are also several shrubs at Agate including buffalo berry, willows, and sumac. Trees and shrubs grow mostly in the wetland areas but sumac is found in the prairie. Shrubs can be distinguished by size, though some shrubs grow very tall, and by the number of branches. Trees generally have one main stem or trunk, while shrubs have several stems growing upwards with shoots coming off. The riparian area supports many large cottonwoods and smaller willows.
The cottonwoods provide vital habitat for wildlife such as red-tailed hawks, Swearinger's hawks, great horned owls, and some species of bats. The trees also shade the waters of the Niobrara River, keeping them cool, allowing more oxygen in the water for fish. The willows serve a similar purpose, providing cover and food for rodents and shading the river. Sumac is found on the hillsides throughout the park and is most common in disturbed areas. Buffalo berry bushes are also found in the park, but are most common near the Visitor's Center and Museum. Both are used by rabbits and rodents as shelter from the wind and to hide from predators. Deer do occasionally browse on the shrubs but the plants are adapted to survive and recover quickly.