Although it was ultimately withdrawn, the UIR was designated by the 90th U.S. Congress as among the initial 27 rivers to be included in the National Wild and Scenic River System. A portion of the river and several tributaries are designated as High Quality Resource Waters as explained in the Code of Iowa as “waters of exceptional recreational or ecological significance”. There are 64.2 miles of the UIR and 314 total river/stream miles in the UIR watershed that have been designated by Iowa as State Protected Waters Areas (PWA). The Upper Iowa River has 113 miles designated by the State of Iowa as Class A, Primary body contact.

The UIR watershed is an area of rugged hills and steep topography with diverse land use. The surface water system in this watershed is made up of a complex network of spring fed coldwater trout streams. It contains 29 stream segments designated as Class B Cold Water Aquatic Life and the Iowa DNR, Fisheries Division, is in the process of reclassifying several new segments in the watershed to this designation. The Northeast Iowa River Basin Study (NIRBS) of Iowa and Minnesota, conducted by the U.S. Department of Agriculture in 1986, identified 25 Highest Priority Coldwater Streams. More of these priority streams (9 of 25) are in the UIR watershed than in any other system included in the study. The land area that drains into these 9 priority streams covers more than half of the area included in the total. There are 14 streams in the UIR watershed that are stocked by the Iowa DNR with catchable size rainbow, brown, and brook trout. There are 9 additional streams stocked with fingerling trout that grow to catchable size in the wild. The last known native population of brook trout in Iowa is found in the watershed and 11 of the streams in the watershed have shown natural reproduction of trout.

The Upper Iowa River and its tributaries contribute to the economic health of the region. The waters of Northeast Iowa are a major attraction for anglers and other water recreationists. The Upper Iowa Watershed is noted for its fine fisheries, and the Iowa DNR estimates over 314,000 angler trips per year are made to the Upper Iowa River Watershed stimulating over $29 million dollars of economic activity each year. The Iowa DNR estimates canoeists enjoying the Upper Iowa River generate another $5 million yearly. Local DNR Fisheries Biologists consider these estimates, which are based on the area of the watershed, to be extremely low.