Animal agriculture is a major enterprise in the basin with McDonald, Newton, and Barry counties consistently ranking in the top five annually, for market value of livestock and poultry products in Missouri. Waste management and disposal at these facilities, wastewater treatment and disposal at associated processing plants, and increasing pollutants in basin streams has become a concern in the Elk River basin. Non-point source pollution in the basin comes from various sources including urban development and runoff, mining, land conversion from forest to pasture, free ranging livestock, channelization, road construction, and septic tanks. Point source pollution sources include sewage treatment plants, poultry processing plants, landfills, industrial discharges, and animal feeding operations. The Elk River basin is included in the Ozark-Neosho aquatic community division.
Streams tend to be very clear with rock and gravel substrates.
Fish and other aquatic fauna unique to this area include redspot chub, bluntface shiner, cardinal shiner, southwestern mimic shiner, western slim minnow, Neosho madtom, Arkansas darter, Neosho orangethroat darter, redfin darter, channel darter, yellow mud turtle, Neosho midget crayfish, and Neosho mucket mussel. Seventy species of fish have been collected from the Elk River basin in Missouri. There are no fish sample records from the time period 1965-1982 for the Elk River basin. Fifty-nine species were collected prior to 1982. Eleven of these species have not been collected since 1965.