The Upper Iowa River is a 156-mile-long tributary of the Mississippi River in the upper Midwest of the United States. Its headwaters rise in southeastern Minnesota, in Mower County near the border with Iowa. It then flows through the Iowa counties of Howard, Winneshiek, and Allamakee, and finally into the Upper Mississippi River near New Albiā¦The Upper Iowa River is a 156-mile-long tributary of the Mississippi River in the upper Midwest of the United States. Its headwaters rise in southeastern Minnesota, in Mower County near the border with Iowa. It then flows through the Iowa counties of Howard, Winneshiek, and Allamakee, and finally into the Upper Mississippi River near New Albin, Iowa. Along its course, it passes through the Iowa cities of Chester, Lime Springs, Florenceville, Kendallville, Bluffton, and Decorah. Its watershed comprises nearly 641,000 acres.