There are three main areas on the upper portion of the river that provide excellent opportunities for wade fishing. They are:
1) Yellowstone Park between Madison Junction (where the Gibbon and Firehole rivers join to form the Madison) and Long Riffle seven and a half or eight miles downstream toward West Yellowstone.
Then again from the Riverside (The Barns) turnoff to the confluence with Hebgen Lake. The river moves away from the road here and splits into many channels, providing an assortment of fishing opportunities. This area tends to be less crowded because access is more difficult.
2) Between Hebgen Lake and Quake Lake. This is an extremely popular section that is open to fishing year round. The upper portion contains mostly pocket water behind boulders and along the edges of the river.
Short accurate casts and lots of mending are required to get the fly into feeding lanes and to present a dead drift.
The lower portion of this section, just before the river empties into Quake Lake, presents some beautiful, deep runs and holes. We caught rainbow after rainbow fishing the seams between the slower and faster water in this area.
There is quite a bit of junk (pieces of bridges, old cabins, dead trees and other debris) left over from the earthquake and resultant landslide (mountain slide - the whole mountain came down) that formed Quake Lake. It makes you wonder when the next big one will hit!
3) The section of the Madison below Quake Lake Dam (the Slide Area) downstream to a miles or so below Three Dollar Bridge.
This section contains some great pocket water and a good number of fat rainbows. However, the river is fast and furious and wading is extremely difficult. Stay close to the bank and be careful. Again, short, accurate casts and lots of mending are necessary to get the fly to the fish. If you fish downstream from Three Dollar Bridge, stay on the north side. The river breaks up into channels on that side and there are more fishing opportunities there.
The rest of the river will be the subject of another story. Unless you have the whole summer off, these three areas should more than keep you plenty busy catching some big rainbow and brown trout.