For angling purposes, the Madison can be divided into four distinct sections.
Madison River in Yellowstone National Park
Madison River near Seven Mile (11 km) bridge
The 19 miles (31 km) of the Madison in the park, although easily accessible, is not suited for beginners and offers technical dry fly and nymph fishing for rainbow and brown trout averaging from ten to fourteen inches (356 mm), with an occasional 20-incher. Most of the river inside the park resembles a large spring creek and has been called the world's largest chalkstream.
The Madison is an early summer and fall river and offers poor fishing in midsummer because of high temperatures contributed by the Firehole. Fishing in the fall is excellent when significant numbers of brown and rainbow trout enter the river from Hebgen Lake. These are usually taken with large streamer patterns. Many pools and runs on the Madison have angler-given names reminiscent of eastern trout stream and British salmon rivers—The Barns, Beaver Meadows, Grasshopper Bank, Cable Car Run and Baker's Hole,.
The Madison River is fly fishing only in Yellowstone National Park and all fishing is catch and release.
Yellowstone National Park Boundary to Quake Lake
After the Madison River takes its leave from Yellowstone Park, it meanders out into the beautiful ranch lands of southwestern Montana. It is here that its true character is revealed and its reputation as a world-class fishery is secured. The Madison rolls majestically through cottonwood lined banks and over riffles and quiet runs that harbor large rainbows and trophy browns. The Madison River flows along Yellowstone’s West Entrance road into Hebgen Lake outside the park. In 1959, the Hebgen Lake earthquake formed Quake Lake just downstream from Hebgen Dam.
Upper Madison- Quake Lake to Ennis Lake
Madison River at Ennis in January
Directly below Quake Lake a three mile (5 km) long whitewater section resulted from the 1959 earthquake. It is characterized by a steep gradient of river including large boulders with Class V whitewater.
Below the whitewater section the river turns into a swift flowing but gentle river for 53 miles (85 km) to Ennis lake. This section has often been called the Fifty Mile Riffle and provides the best fly fishing on the river. There is a part of the Madison River in this section that is only open to wade fishing. Guide boats are allowed to float through this section but are not allowed to fish from the boat. This area extends from 3 Dollar Bridge all of the way to Lyon Bridge.
Lower Madison- Ennis Lake to Three Forks
Lower Madison River Near Black's Ford access, September
Trout Unlimited — Trout Unlimited's mission is to conserve, protect and restore North America's coldwater fisheries and their watersheds.
Western Watersheds Project — The mission of Western Watersheds Project is to protect and restore western watersheds and wildlife through education, public policy initiatives and litigation.
Montana River Action — The clean flowing waters of Montana belong to the people and are held in trust by the State for a pollution-free healthful environment guaranteed by our Montana Constitution. Montana River Action's mission is to protect and restore rivers, streams and other water bodies.
Madison River Foundation--- The mission of the Madison River Foundation is to preserve, protect, and enhance the Madison River watershed. 
^Mathews, Craig; Molinero, Clayton (1997). The Yellowstone Fly-Fishing Guide-A authoritative guide to the waters of Yellowstone National Park. Guilford, CT: The Lyons Press. pp. 37–40. ISBN1-55821-545-X.
^Parks, Richard (1998). Fishing Yellowstone National Park. Helena, MT: Falcon Press. pp. 30–34. ISBN1-56044-625-0.
Back, Howard (1938). The Waters of the Yellowstone with Rod and Fly. New York: Dodd & Mead.
Parks, Richard (1998). Fishing Yellowstone National Park. Helena, MT: Falcon Press. ISBN1-56044-625-0.
Brooks, Charles E. (1979). The Living River-A Fisherman's Intimate Profile of the Madison River Watershed--Its History, Ecology, Lore and Angling Opportunities. Garden City, NJ: Nick Lyons Books. ISBN0-385-15655-3.
Mathews, Craig; Molinero, Clayton (1997). The Yellowstone Fly-Fishing Guide-A authoritative guide to the waters of Yellowstone National Park. Guilford, CT: The Lyons Press. ISBN1-55821-545-X.
Brooks, Charles E. (1984). Fishing Yellowstone Waters. Clinton, NJ: New Win Publishing Inc. ISBN0-8329-0353-1.
Holt, John (1996). Montana Fly-Fishing Guide-East. Guilford, CT: The Lyons Press. ISBN1-58574-529-4.
Holt, John (1993). River Journal - Madison. Portland, OR: Frank Amato Publications. ISBN1-878175-27-0.