Upper Klamath Refuge comprises 15,000 acres, mostly freshwater hardstem-cattail marsh and open water, along with 30 acres of forested uplands. These habitats serve as excellent nesting and brood rearing areas for waterfowl and colonial nesting birds, including American white pelican and several heron species. Bald eagle and osprey nest nearby and can sometimes be seen fishing in refuge waters.

A 9.5-mile self-guided canoe trail meanders through the Upper Klamath Marsh and is an ideal way to observe marsh habitats and bird life. The trail has four segments: Recreation Creek, Crystal Creek, Wocus Cut, and Malone Springs.

These segments can be accessed from either the Rocky Point or Malone Springs boat launches. The Rocky Point boat launch has a barrier-free toilet, boat dock, and fishing dock to serve people with disabilities. Canoes may be rented from nearby concessionaires.