The exceptional fishery comes from the river's role as a living laboratory for wild trout management. In 1968, the Montana Department of Fish, Wildlife, and Parks (FWP) initiated a study on the stocking program on trout populations. Researchers found that the addition of thousands of hatchery-reared trout each spring was reducing the fish counts. Montana FWP fisheries researcher Dick Vincent concluded the hatchery fish were displacing the resident population from the holding areas. However, the hatchery fish were unable to survive more than a short time in the demanding river environment.
The results, and subsequent fallout, were felt all across Montana. Consequently, most rivers and streams in the state were then converted to wild trout management (natural reproduction only) with spectacular improvements in the quality of trout fishery.
For the Madison, elimination of stocking was only the first of a series of steps designed to improve the fishery. Next in line was dealing with angling harvests. Creel surveys and population censuses indicated that anglers were keeping so many of the larger trout that, despite good reproduction, only small fish remained. The average fish size had dropped to about 10 inches.
Scores of sportsmen demanded the restoration of quality fishing, the Montana Fish and Game Commission designated the 30 miles of the upper Madison from Quake Lake to Varney Bridge as a "catch-and-release" section for artificial flies and lures only. Because of this trout populations have more than doubled since the advent of the special regulations in 1977. Numbers of 13- to 18-inch fish have risen even more sharply, and are now estimated at more than 800 per mile.
In the early 1990s whirling disease was detected on the “upper Madison” (the “upper” typically referring to this stretch, meaning upstream of Ennis). Because the number of rainbows declined, brown trout were there to fill in the gap. It is believe there are between 800 browns and 500 rainbows per mile in this stretch, and many local folks think these numbers are conservative. These numbers appear to be holding steady and, in fact, most local outfitters think the number of large brown trout is a high as it was in the twenty-plus years ago!