[7] The headwaters of the Redwood River are in Aetna Township in northeastern Pipestone County, approximately four miles (6.4 km) west of Ruthton, on the Coteau des Prairies, a morainic plateau dividing the Mississippi and Missouri River watersheds.

In Redwood Falls, the county seat of Redwood County, the river enters the wooded valley of the Minnesota River, falling 100 feet (30 m) in one mile (1.6 km) over granite ledges in Alexander Ramsey City Park.

[7][8][9] Principal tributaries of the Redwood River include Coon Creek, 37 miles (60 km) long, which flows from Lake Benton in Lincoln County westwardly to Russell in Lyon County; Three Mile Creek, 50 miles (80 km) long, which rises in Lincoln County and flows northeastwardly and southeastwardly through Lyon County, joining the Redwood downstream of Marshall; and Ramsey Creek, 10 miles (16 km) long, which flows over a waterfall in Ramsey City Park in Redwood Falls.

[3][9][8] Approximately 82% of the land in the Redwood River watershed is used for agriculture, primarily for the cultivation of corn and soybeans.

Hundreds of miles of streams in the watershed have been converted to agricultural ditches, disrupting habitat and reducing the ability of the land to absorb flooding.