Fly Fishing on the Madison River

Angler John Lewton casts a line onto the Madison River, west of Bozeman, in this 2015 photo.

Officials have confirmed that the parasite that caused a die-off of mountain whitefish in the Yellowstone River exists in at least seven other rivers in the state.

Montana Fish, Wildlife and Parks biologists said Wednesday that the parasite has been confirmed in the upper and lower Madison, East Gallatin, Bighorn, Stillwater, and Boulder near Big Timber. The parasite had already been confirmed in the Jefferson and Shields rivers.

The results don’t come as much of a surprise to state biologists, who have said before that they expect the parasite has spread farther than they know. Travis Horton, the regional fisheries manager for FWP, said the agency is working on a statewide effort to figure out where the parasite is. They are also trying to figure out what strain of the parasite is present and whether different strains are in different streams.

“There’s still a lot that we need to learn about what this thing is going to do,” Horton said.

Other than in the Yellowstone, fish deaths linked to the parasite have not been documented this year in any of the rivers where its presence has been confirmed. A number of whitefish were found dead in the Jefferson River last year, but officials are unsure if the parasite was definitely the cause.

The microscopic parasite causes proliferative kidney disease, one of the more devastating conditions for whitefish and trout. It has caused fish kills in the Snake River system in eastern Idaho in the last five years. Before this year, it was found twice in Montana — in a reservoir in the Smith River drainage and on Cherry Creek, a tributary of the Madison River. No fish deaths were recorded in either case.

This past August, FWP confirmed the deaths of at least 4,000 whitefish due to the parasite in the Yellowstone River this fall. A few trout were also found dead, but they estimate the total death toll for whitefish to be in the tens of thousands. Officials shut down recreation on a wide swath of the river in response. The closure ended about a month ago.

The parasite can easily be spread between river systems on gear or animals. FWP began taking samples from other streams soon after the fish kill started. Samples from the main Gallatin River were negative, as were some from a few tributaries of the Yellowstone. Samples from the Missouri and Smith rivers have not been analyzed yet.

What happened on the Yellowstone River won’t necessarily happen on all of the other rivers, though. Low flows and high water temperatures likely exacerbated the fish kill on the Yellowstone, but not all rivers experience the same conditions that one does.

“All these rivers are going to act differently because of their flow regimes, temperature regimes,” Horton said.

Bruce Farling, the executive director of Montana Trout Unlimited, said the presence of the parasite means people need to begin taking action to keep rivers healthy in hopes of staving off a potential kill.

“We’ve got to have cooler water in our rivers,” Farling said. “Warm water really amplifies this problem.”

Montana Democratic U.S. Sen. Jon Tester sent a letter to the U.S. Army Corps of Engineers this week asking them to consider starting studies or projects that would “enhance natural riverine processes, protect riparian areas, restore instream flows, and achieve other ecosystem restoration benefits that help mitigate extreme weather events in the Yellowstone and its tributaries.”

Horton said FWP would be “more than happy to engage and work on those things” with the Army Corps.

Michael Wright can be reached at or at 582-2638. Follow him on Twitter @mj_wright1.