The Refuge has 3 hiking trails. The Mill Butte Trail is a 4.5 mile loop that starts at Refuge Headquarters. The summit is 2,619 feet with a 360 degree view. The trail is rated moderately difficult.
The McDowell Marsh Environmental Education Trail is a 1.2 mile loop that starts at River Camp. The first half of the trail is wheelchair accessible and has a boardwalk over a wetland. The accessible trail continues around the Marsh to McDowell Lake. At this point the trail narrows and gains elevation as it goes through a forested area. The trail is rated easy.
The Beaver Pond Overlook Trail and the Big Pine Trail share a trail head on Rookery Road. The Overlook Trail is a .25 mile spur that follows an old road grade to an interpretive viewpoint overlooking the Beaver Ponds. The Big Pine Trail is an easy .75 mile loop through a mixed species forest.