The trail's southern node is the Mexican border near Antelope Wells, New Mexico. The trail shoots north through the desert into the Gila National Forest and the Aldo Leopold Wilderness. It then crosses the El Malpais National Monument, picking up the 1,000-year-old Zuni-Acoma trade route. Before reaching Colorado, the trail travels through the Cibola National Forest and the Carson and Santa Fe National Forests.

Entering Colorado from the south, the Trail passes through remote, rugged alpine terrain like the South San Juan, Weminuche, and La Garita Wilderness Areas. There are several crossings of the Continental Divide and the Colorado Trail; for over 100 miles, the routes of the CT and the Continental Divide Trail are contiguous. The trail is almost entirely on national forest land, including San Juan, Rio Grande, San Isabel, Gunnison, White River, Pike, Arapaho, and Medicine Bow-Routt. A chunk of the trail passes through Rocky Mountain National Park and the Mt. Zirkel Wilderness.

The trail ventures into Wyoming at Routt National Forest. It then crosses BLM land before reaching the Bridger-Teton National Forest and the Popo Agie and Fitzpatrick wildernesses. From there, it's on to Yellowstone National Park.

The trail crosses into Idaho at the Targhee National Forest. It stays close to the Montana border, and after it finally jumps the line, users get to explore the Salmon National Forest, Anaconda-Pintler Wilderness, and Helena National Forest. The trail transverses the Scapegoat, Bob Marshall, and Great Bear Wildernesses. Finally, after passing through Glacier National Park, the trail ends at the Canadian border.