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The Wapsipinicon River stretches over 290 miles from the Iowa/Minnesota border all the way to the Mississippi River near Clinton, Iowa. Although it only extends two miles into Minnesota, the Wapsipinicon River is the fifth largest Iowa tributary of the Mississippi, being surpassed in length only by the Des Moines, Cedar, Iowa, and Skunk rivers. It is a long narrow watershed that for 180 miles averages barely more than 15 miles wide and thus it has no major tributary.

Even though it is narrow, this watershed covers 4.5% of Iowa. The Wapsipinicon River boasts the longest, continuous stretch of natural and scenic river corridor in the Iowan Surface Region of Iowa. Much of that river corridor is in public ownership and dominated by wooded wetlands and riparian forests that provide habitat for birds, reptiles and other animal species, as well as birders, boaters, paddlers and anglers.

The Upper Wapsipinicon River, or Upper Wapsi, is a section that includes the 270 miles of river above Anamosa, Iowa. The Upper Wapsi Watershed drains over 1 million acres and encompasses all or portions of 11 counties, 27 communities, 17 unincorporated villages, 120 lakes and 8 major rivers and streams totaling over 2,000 river miles.