It almost goes without saying...the Madison River is the most famous of all of the rivers in Montana. Aside from its incredible beauty, the fly fishing opportunities abound through virtually every mile from its origin in Yellowstone National Park to the confluence with the Jefferson and Gallatin to form the headwaters of the Missouri River...a total of over 180 miles.
The Madison defies any single description. The upper section (from its headwaters at the confluence of the Firehole and Gibbon rivers to Hebgen Lake) has been described by many as a "large spring creek". The water is relatively slow and clear and the wading is, for the most part, relatively easy when compared to most of the lower sections. The waters from the Firehole are very rich with minerals and nutrients as a result of its source...a series of thermal geysers. As a result, both the river's inhabitants...aquatic insects as well as the surrounding lands are very well nourished. This upper section is also one of the very best places in YNP to observe the wildlife. Bison, elk and moose are common and numerous and often cause traffic jams along the road that parallels most of this secion. I think it can be safely said that the very best fishing is in the spring and early summer and again in the fall. The hotter summer months cause the water to warm enough that many of the fish retreat to the colder deeper waters of Hebgen Lake. In the spring and early summer, many large rainbows from Hebgen Lake enter the Madison to spawn. In the fall, the brown trout become much more numerous as they come into these waters to spawn. There are certainly resident populations of both rainbow and brown trout present year around but spring/early summer and the fall starting in September are the two most productive times for the fly fisher. The very early season is mostly nymphing followed by casting large salmonfly dries long the banks. As fall approaches, the fishing turns more toward swinging streamers and soft hackle flies for the lake run brown trout. There are numerous fly shops in West Yellowstone that will be happy to provide you with information on seasonal hatch information and many of them provide fishing reports and other YNP fly fishing information via their online resources. Over the years, my go to source for current information regarding fly fishing in YNP has been Blue Ribbon Flies in West Yellowstone. They are generally up to date with their fishing reports and hatch information. Here is one of the best articles I have found on YNP hatches. It is Fishing Yellowstone Hatches - Revisited by John Juracek and it is on the Blue Ribbon website.
Next, the river flows into Hebgen Lake (16 miles long) then through a short (1-2 mile) fast water section between Hebgen dam and into Quake Lake. Both Hebgen Lake and Quake Lake have large populations of both rainbows and browns. The short section between the two lakes is not often fished as the access is poor compared to most of the river.
Once the river leaves Quake Lake, it becomes the river most of us envision when "the Madison" is mentioned. Some call it the "50 mile riffle". I have considerable experience in the section between Quake Lake and the town of Ennis. Here, the water increases in speed and the wading becomes considerably more difficult. Much of the bottom is relatively large smooth (slick) rocks from baseball size to the size of your car. Wading the edges or fishing from the banks is relatively easy but wading into the heavier current is tough and not for most fly fishers. I have taken more "swims" in the Madison than in all the others rivers I have fished combined. Fishing access becomes a bigger issue here as well and that is the primary reason the floating is so very popular in much of this section. Most of the wade fishing access is located where the five or so bridges cross the river. The upper bridge is the Highway 87 bridge and the lower most is Ennis bridge. Highway 87 comes in from the Henry's Lake area of northeastern Idaho which is also the headwaters of the famed Henry's Fork. It is just over an hours drive from the Harriman State Park (aka Railroad Ranch) area in Last Chance, Idaho. There are two sections between Quake Lake and Ennis that are "closed to fishing from boats". They are the section from the 87 bridge to Varney bridge and the section from Ennis bridge to the town of Ennis. This does not mean that you will not see boats, you just cannot fish from a boat in these sections. This map (compliments of anglerguide.com) will provide most of the access information.
For specific and up-to-date hatch and fishing reports for the section between Quake Lake and Ennis, almost any fly shop in the southern half of Montana will be able to help. My personal preferences are Kelly Gallop's Slide Inn fly shop for the upper reaches and Madison River Fishing Company and Trout Stalkers for information on the sections closer to Ennis.
I will be honest and say that I have very little experience on the Madison in the stretch between Ennis and Three Rivers. Aside from just an hour more driving, the Quake Lake to Ennis section I discussed above have kept me more than satisfied in my 40+ years of fishing the Madison. Many describe this as the "lower" section. I do know that Ennis Lake has a considerable influence on this section of river and make it somewhat "seasonal" in nature. During the warmer summer months starting as early as June, the warm water released from Ennis Lake increases the water temperature and the trout become much less active and stay "hunkered down" much more than the rest of the river above Ennis Lake. Aside from these few warmer months, I understand the fishing can be quite good. In addition to the three fly shops I mentioned in the last paragraph, I will add another for this lower section. It is The River's Edge and they provide a good fishing report on this section.
Here are links to more information:
The Madison River - Big Sky Fishing
More on the Madison River - Firehole Ranch
Fishing Map - Hebgen Lake to Three Forks - Anglerguide.com
Fishing Map - Upper Madison (Firehole to Quake Lake) - destinationmontana.com
Madison River Fly Fishing Tactics - by Madison River Fly Fishing