[7] Due to ongoing skirmishes between the Pillager Chippewa and the Dakota Sioux, the Winnebagoes were in constant danger, so they requested relocation to southern Minnesota, near Mankato, and in 1855 ceded the land to the United States.

By the mid-1860s several settlements from the present site of Long Prairie to Motley were prospering, using flatboats, and for a very short time even a steamboat, for transportation and shipping.

In 1855 the Winnebago had been moved to a reservation in Blue Earth County in southern Minnesota, and the lands were sold to investors from Ohio.

At the end of the Civil War the communities west of Long Prairie were settled by Southern soldiers who had fought for the Union Army that were not very welcome in their home state of Kentucky.

At the time of Todd County's original European settlement, the forested areas of the Long Prairie River watershed were substantial.

As most of the trees were harvested, the sandy soils in these areas were left unprotected, increasing erosion, and gradually filling the streams with sediment.

Industry located along the riverbanks and used the river as a source of water and as a discharge point for the waste materials generated by their companies.

In the dry years of the late 1970s, many irrigation systems were shut down at critical times because of low surface water levels.

To this day, irrigation systems are flourishing in the deep water-rich sands of the Long Prairie River Valley, but by 1994, only 14 surface water permits still existed in Todd County.

[12] The Long Prairie River and its watershed were influenced and shaped by a Glacier that covered the region at various intervals during the late Pleistocene.

[4] According to the Minnesota Pollution Control Agency, 41% of the Long Prairie River's watershed below Lake Carlos is used for agriculture; the main crops are potatoes, corn, soybeans and alfalfa.

[8] At the United States Geological Survey's stream gauge in the city of Long Prairie, the annual mean flow of the river between 1972 and 2005 was 166 cubic feet per second (5 m³/s).