Lake Superior - North Rainy River - Headwaters Lake Superior - South Vermilion River Nemadji River Cloquet River Pine River Rainy River - Rainy Lake Little Fork River Mississippi River - Headwaters Leech Lake River Upper St. Croix River Root River Big Fork River Mississippi River - Winona Upper/Lower Red Lake Kettle River Mississippi River - Lake Pepin Mississippi River - Grand Rapids Mississippi River - La Crescent Crow Wing River Otter Tail River Mississippi River - Reno Mississippi River - Brainerd Zumbro River Redeye River Upper Big Sioux River Mississippi River - Twin Cities Snake River Des Moines River - Headwaters St. Louis River Rum River Lower Big Sioux River Lower St. Croix River Cottonwood River Minnesota River - Headwaters Cannon River Mississippi River - St. Cloud Long Prairie River Lake of the Woods Lower Rainy North Fork Crow River Mississippi River - Sartell Lac Qui Parle River Buffalo River Wild Rice River Minnesota River - Mankato Sauk River Rock River Redwood River Snake River Chippewa River Watonwan River Clearwater River East Fork Des Moines River Red River of the North - Sandhill River Upper Red River of the North Blue Earth River Red River of the North - Marsh River Roseau River Minnesota River - Yellow Medicine River Le Sueur River Little Sioux River Bois de Sioux River Cedar River Lower Minnesota River Pomme de Terre River Red Lake River Lower Des Moines River Upper Iowa River Red River of the North - Tamarac River Shell Rock River Two Rivers Rapid River Red River of the North - Grand Marais Creek Mustinka River South Fork Crow River Thief River Winnebago River Upper Wapsipinicon River 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% %Altered %Natural %Impounded %No Definable Channel wq-bsm1-06.