Water quality in the three rivers is generally good. Niobrara River water has been monitored and some chemical and physical aspects of Missouri River water have been studied intermittently since before the closure of the large dams. The inflows from the James and Vermillion rivers have occasional high levels of fecal coliform bacteria; however, this has not limited the river's use for primary contact recreation nor is it expected to.

The water quality on the Missouri most affected by dam construction was turbidity. The water became less turbid, or much clearer, after the dams reduced natural sediment transport in the river. High turbidity did not affect the primary energy source of the river, the erosion caused by the main channel meandering, or the runoff from tributaries. The clean water from the dams leads to downcutting, narrowing of the river channel, rapid erosion on the new banks, loss of sandbars, and reduction of nutrients important in fish and wildlife habitat.

Selenium, a naturally occuring heavy metal, is found in eastern South Dakota. The US Army Corps of Engineers conducted an analysis of the Missouri River water and sediment during 1992 in conjunction with a project to create habitat for interior least terns and piping plovers. Sample sites included Niobrara, Nebraska, and Running Water, South Dakota. Results indicated that the amount of selenium was within state water quality standards and Environmental Protection Agency criteria.

The United States Environmental Protection Agency maintains web sites with information pertaining to the Missouri and Niobrara rivers.

Information and resources highlighting the Lewis and Clark Lake Watershed (encompasses the entire "rec river").