Located in the unglaciated "Driftless" region, the Root winds its way through one of the most unique and beautiful landscapes in the country. Fertile bottomlands are flanked by towering limestone cliffs. The Root is a sandy, shallow river for much of its length, and prone to serious flooding in the spring. There are four minor branches of the Root, each a river in its own right, plus the main stem.
The North Branch of the Root, which flows through Chatfield, is a warmwater stream, as is the Middle Branch which joins the North Branch just four river miles downstream of Chatfield. Both are fed by a large number of warmwater and coldwater streams, from rocky smallmouth creeks like Deer and Bear Creek, to fine trouting waters like Money Creek and Trout Run. These two branches both hold good numbers of redhorse, white suckers, northern hog suckers, smallmouth bass, and rock bass. This area is home to the extremely rare Gravel Chub. Both branches are quite small, and easily wadable, although access is spotty. The North Branch, below Chatfield, is a designated canoe route with canoe campsites strategically placed along its length for multi-day floats.
The South Branch of the Root runs from Preston to Lanesboro. The South Branch is all trout water, with naturally reproducing brown trout in the upper section, above Lanesboro, and a mix of browns and stocked rainbows below. Below Lanesboro, suckers are more prevalent. The South Branch joins the North Branch three river miles downstream from Lanesboro to form the Main Stem of the Root.
The Main Stem of the Root runs for an additional 55 miles from the confluence to the Mississippi River. Here the river takes on the character which makes the Root such an excellent roughfishing stream. The main stem of the Root is nestled in a wide valley filled with farms, small towns, and wide swaths of hardwood forest. The upper section, from Whalen to Rushford, produces huge runs of silver redhorse, mooneye, hogsuckers, brown and rainbow trout, and many other fish. Past Rushford, the species mix changes, with the trout and hogsuckers being replaced by drum, carp, catfish, goldeyes, and shovelnose sturgeon. The Minnesota State record goldeye was caught in the main stem of the Root. River access is good, and travel by canoe is popular. Portions of the river are wadeable, but even in low water the river is almost impossible to cross on foot.
Downstream from Houston, the seldom-fished South Fork of the Root augments the flow of the main stem. The South Fork is trout water in its upper reaches, but the lowest twenty miles or so is the domain of the hogsucker. Crystal clear, shallow, rocky water makes sight-fishing for hogsuckers possible in this part of the river.
Below Houston, many species of fish from the Mississippi River may be found. Channel Catfish are a popular target, and white bass, walleyes, buffalo, and even gar stray into the lower Root at certain times of the year. Finally, the Root joins the mighty Mississippi in the Upper Mississippi Wildlife and Fish Refuge just across the river from LaCrosse, Wisconsin. Here, an endless maze of running sloughs stretches for miles.
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