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A flash flood that destroyed homes in Baldwin, Wis., and killed a motorist in St. Croix County on June 29 ripped through the Rush River Valley with historic force, but fish experts say the river’s esteemed trout population appears to be all right.

Newly born trout likely suffered high mortality rates, but juvenile fish and adult trout should have been able to find refuge near the bottom while top waters rose 10 to 12 feet above normal in some places, said officials from the Wisconsin Department of Natural Resources and Trout Unlimited.

“In general, adult fish can hang on really good,’’ said Kasey Yallaly, a DNR senior fisheries biologist based in Baldwin. “They go to the closest stable cover until it recedes.’’

But trout hatched this spring, probably got hit as hard as they have in other historically bad floods in western Wisconsin’s Driftless Area. But even at that, Yallaly conducted surveys this month on a few tributaries of the Rush River, and said she found good numbers of juvenile and baby fish.

The DNR also checked sites where conservation dollars have been spent over the past 20 years to fortify stream banks and make other trout stream habitat improvements. All those structures remained intact, she said.

The worst damage to stream banks happened in the lower reaches of the 35-mile river as it approaches the Mississippi River just north of Maiden Rock, Yallaly said. The river’s headwaters are south of Baldwin and the best fishing is in the river’s middle reaches.

“It looks like somebody set off dynamite,’’ she said.

Even after the floodwaters receded, some high banks in the area along County Road A beside the lower Rush were actively eroding and dropping unwanted sand and silt into the river, she said, and fallen trees were everywhere. Some restoration work may be needed, Yallaly said, but the DNR doesn’t have much in the way of easement rights to work in the affected area.

“We would like to for sure because there’s a lot of trophy fish there,’’ she said.

Del Brisson of Cottage Grove owns a parcel of recreational land along the Rush in the small town of El Paso, a place where the river breached high banks and rose another 6 to 8 feet in a matter of a couple of hours after sunrise June 29.

Brisson’s son, Jared, had parked a 7,000-pound, 24-foot fifth-wheel trailer on the land for temporary safekeeping and it was swept away along with a neighbor’s 500-gallon propane tank. The tank geysered propane and water upward as it sailed downstream. The trailer’s frame was later found wrapped around a nearby bridge pillar.

“We were told it was the worst flooding in El Paso since 1965,’’ Brisson said.

Yallaly said the El Paso Rod and Gun Club lost a trap house in the flood, but the rocky stream banks in the area held steady. She said the Rush is home to one of the strongest trout populations in Wisconsin, carved out of rocky terrain at the floor of a steep valley for much of its route.

In the late 1800s, commercial fishermen netted tons of trout from the Rush to supply restaurants in St. Paul, according to a 2002 DNR study of the river. The study said the river’s cold water fish community was healthy, but brown trout were taking territory away from native brook trout. The Rush has many riffles and meanders with deep bends and good cover for fish to hide. It’s low temperatures and rocky bottom support natural reproduction of trout.

Scott Wagner, president of the Kiap-TU-Wish Chapter of Trout Unlimited, said property losses above stream level, including small bridge failures, were tremendous along the Rush. To the west, the same flood wreaked havoc along the Trimbelle River and parts of the Kinnickinnic.

But for a stream bed as durable as the one holding the Rush River, Wagner said, a massive flash flood like the one June 29 can rejuvenate what’s below stream level. The surging water scours and lifts undesirable sand and silt deposits, washing them out to expose the river’s original, hard-bottom substrate. Those rocks and gravel provide critical spawning habitat for trout and a good home for aquatic bugs and crustaceans to thrive. Moreover, there’s less debris to clog underground springs that feed into the river.

Wagner likened the flood to a wildfire restoring native plant life across a prairie.

“Above stream level it can look pretty bleak,’’ Wagner said. “But the banks [of the Rush River] are so well anchored for the most part. It’s cut deep into the bedrock.’’

He said part of Kiap-TU-Wish’s agenda for now is to install rock structures on certain area trout streams that lack durable banks. In high water events, the improvements ideally will help flush out stream bottoms softened by years of runoff.

Tony Kennedy • 612-673-4212