An EPA inspection in that state in December 2013 noted phosphorus and other discharges from production areas of the 2,200-head facility in a nearby waterway.
The agency said Winifred Feed Lot had also failed to develop and implement a Nutrient Management Plan (NMP), as required by it under its permit issuing function.
Such management plans are critical to ensuring that nutrient-rich manure is applied properly and kept out of nearby river and streams, said the EPA.
"Manure and wastewater discharges from concentrated animal feeding operation production areas can violate water quality standards, as well as pose a risk to human health, threaten aquatic life and its habitat, and impair the use and enjoyment of waterways," says the agency.
Winifred Feed Lot said it is now in compliance with the CWA in terms of developing and submitting a NMP.