The refuge has four paddling trails starting at the end of Buffalo City Road. There is a canoe/kayak launch and parking for vehicles, including those with trailers, at the end of the road (note that parking can fill up quickly during peak summer season). There is another canoe/kayak launch and additional parking on Milltail Road where it meets Milltail Creek.
Trails are marked by white posts with color-coded markers showing where trails change directions and/or intersect other trails. The red paddling trail is 1.5mi and loops around a small island near the Sandy Ridge trails. The green trail is 2.0mi one-way and travels up to Sawyer Lake. The yellow trail is 4.0mi one-way and travels down Milltail Creek to Alligator River. The blue trail is 5.5mi one-way up Milltail Creek to the second canoe/kayak launch on Milltail Road.