"Montana's Madison River has long been one of the most famous and revered rivers in the world. The river often is listed as the number one trout river in North American and appears in books with titles like "50 places to fish before you die". In the mid 90s everything changed for the river when a microscopic invader had a devastating impact on the river. Whirling disease is a small microbe that affects rainbow trout. The parasite causes deformation in the spinal cord of young trout that causes them to swim in circles, usually resulting in death. In some reaches of the river, mortality of rainbow trout reached levels over 90%. News of the outbreak quickly spread throughout the angling community and the number of fisherman visiting the river drastically decreased. The Madison river became the poster child for whirling disease and the microbe quickly hitchhiked to other rivers around the West producing similar results. Some states, like Colorado, tackled the problem by stocking rainbow trout fingerlings. In Montana, where there all trout in rivers are wild and there is not a hatchery program, fisheries biologists decided to let nature run its course. The gamble paid off, and the trout that did survive the initial massive die offs began showing some resistance to the disease.
Today the Madison River has returned to greatness, and although whirling disease is still present in the river, rainbow trout levels have rebounded to pre whirling disease levels. The Madison is once again one of the favorites of Montana fly fishing guides and outfitters. Many guides also feel that the brown trout fishing in the river is better than it has ever been with numerous fish over 20" frequently being caught. Each of the last few years a few lucky fisherman have managed to hook and land monster browns the taped at over 30" and weighed over 10lbs."
https://www.montanaangler.com/madison-river-fly-fishing/madison-fishing-article#:~:text=In%20the%20mid%2090s%20everything,circles%2C%20usually%20resulting%20in%20death.
