TROUBLE ON THE UPPER MISSOURI.(rainbow trout numbers)

LAST OCTOBER, when biologists counted fish in the Missouri River above Cascade, Montana, they found record numbers of big, heavy rainbow trout. "Off the chart" was the notation for one section of the river that outdoor writers were calling the best trout stream in America. And the fish were in tremendous condition; huge.

"They always are heavy," says George Liknes, a fisheries biologist for Montana Fish, Wildlife & Parks. "These were like pond fish. You had to use two hands to handle them and get their lengths. It actually slowed us down."

But there was something missing on the Upper Missouri. Scientists didn't find many little fish--the fish that grow up to be big fish, the fish needed to sustain the historic population of rainbow trout anglers found there last year.

Whirling disease, confirmed three years ago in the Missouri River below Holter Dam, is taking its toll. Populations of two-year-old and older rainbow trout were up 200 percent over the historic long-term on one stretch of the river and 300 percent on another. Biologists estimate that 38 percent of the long-term historic number of yearling rainbow trout survive in the Craig section of the Missouri and 73 percent survive in the Cascade section.

"The infection rate and intensity of whirling disease have risen on the Missouri," Liknes says. It was already quite high in …