Many years ago, long before today’s Root River State Trail was created, the right-of-way between Fountain and Houston, Minnesota, was once part of the massive Chicago, Milwaukee, St. Paul & Pacific Railroad network (a.k.a., Milwaukee Road). The company is regarded as one of the classic “fallen flag” lines and boasted a system that once spanned more than 10,000 miles, from Chicago to Seattle and with sprawling secondary and branch lines throughout the Midwest. Today’s trail was once part of this Midwestern trackage that served primarily agricultural interests, its earliest history tracing to the mid-19th century just before the Civil War. The Milwaukee Road gained control of the property during the latter 1800s and operated it until a bankruptcy in the late 1970s, when the line was abandoned. During the 1980s, it was converted into a trail, much of which is now paved.

The history of trains using the right-of-way that is now the Root River State Trail can be traced back to the Root River Valley & Southern Minnesota Railroad (RRV&SM), chartered on March 2, 1855, to connect the hamlet of Hokah along the Root River (and not far from the mighty Mississippi River) in the Minnesota Territory with the Dakota Territory. The concept for this new transportation artery came by way of Colonel T.B. Stoddard, which had arrived in La Crosse, Wisconsin, in 1851. He envisioned a great rail bridge over the Mississippi linking that town with the Minnesota Territory, stretching through its southern lands. His grand plans were of reaching as far west as the Rocky Mountains and Pacific Coast. As early as 1852, he began acquiring land for his railroad, which led to the 1855 chartering of the RRV&SM. Unfortunately, nothing ever came of this despite having $5 million in capital stock.

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After almost 10 years, Stoddard was granted a second charter on March 4, 1864, to construct the Southern Minnesota Railroad (SMRR), whose new eastern terminal would be Grand Crossing across the Mississippi River from La Crosse. Two years later, the SMRR began actual construction in 1866 and reached Rushford a year later. During 1868, Lanesboro was connected as was Wells by 1869. In 1870, the SMRR had laid track as far as Winnebago, a distance of 167.5 miles. This was the farthest west the railroad would reach. In 1871, Stoddard gave up the SMRR presidency, and in 1876, a bridge was finally built over the Mississippi, eliminating car ferry operations across the river with the Chicago, Milwaukee & St. Paul (CM&StP).

As the CM&StP continued its expansion throughout the Midwest, it acquired full control of the SMRR in 1880, renaming it as its Southern Minnesota Division. Upon this takeover, the new owner moved the connection across the Mississippi River at Grand Crossing to La Crescent. As the CM&StP grew, it eventually extended the railroad from Winnebago all the way to Wessington Springs, South Dakota, adding several branches along the way. Additionally, secondary lines were built connecting to its Rapid City route and St. Paul–Minneapolis.

A 1925, bankruptcy renamed the CM&StP as the Chicago, Milwaukee, St. Paul & Pacific Railroad, upon which time it adopted its nickname the Milwaukee Road. While the system reached the Seattle and the Pacific Northwest, it is often regarded as a “granger road” because of the significant agricultural items it moved across the Midwest. Today’s Root River State Trail was one of the railroad’s lines that derived much of its freight from this industry moving grain, corn, and similar types of products. As the 20th century progressed, particularly after World War II, the Milwaukee (and several other granger lines, such as the Rock Island, Chicago & North Western, and Chicago Great Western) found it more difficult to remain profitable. Trucks and the Interstate highway system pulled away much of the freight the rails had once moved. In a classic economic case of oversupply, significant portions of the Southern Minnesota Division, which included the so-called “Smoky Valley Line” between La Crosse and Austin, had become superfluous by the 1970s. Passenger trains had stopped serving the line after 1957, and as early as the 1960s freight service had been cut back to just three days a week.

During the route’s late era, it was somewhat unique to see freight trains pulled by sets of Electro-Motive SW1 model switchers. These diesels were normally assigned to yard duties and similar chores. Because of the relatively light trackage and bridges used on the route, which also suffered from deferred maintenance and weed-choked rails, the Milwaukee Road found the units ideal in this regard without the need to significantly upgrade the infrastructure. By the mid-1970s, the company’s financial situation continued to worsen, and it began abandoning large chunks of its secondary lines in Minnesota and neighboring states. On December 19, 1977, the railroad filed for bankruptcy (the third in its history). In 1980, it pulled up the rest of the Smoke Valley Line, which literally paved the way in creating today’s Root River State Trail, opening a few years later.

Railroad attractions near the trail include the Jackson Street Roundhouse in St. Paul, Minnehaha Depot and Minnesota Streetcar Museum in Minneapolis, and Trains on the Farm in Clarksville, Iowa. Also, in nearby Wisconsin there is the Colfax Railroad Museum in Colfax.