Water resources are of the utmost importance to the Niobrara National Scenic River. The Niobrara is a favorite vacation destination for outdoor enthusiasts each summer. Most visitors come to canoe, kayak, tube, swim, or fish.
Surface water quality is monitored on a five year rotational schedule by NDEQ. Resource management staff at Niobrara NSR have incorporated a long-term water quality monitoring program since 2001. Ground and surface water quality is generally good. The Nebraska Department of Environmental Quality (NDEQ) rated the Niobrara a Class A, unimpaired waterway. Monthly samples indicated fecal coliform bacterial counts were within standards for water contact recreation. All major bridge crossings are monitored for temperature, pH, dissolved oxygen, turbidity, conductivity, alkalinity, salinity, nitrates/nitrogen, phosphates, and ammonia. Tributaries in the canoeable reach are also included in this monitoring program, however only turbidity, pH, conductivity, and temperature are measured at those locations. E. coli has also been evaluated to determine if fecal coliform bacteria is impacting the river on a seasonal basis.