The giant Boise-based agribusiness J.R. Simplot Company has agreed to pay $775,000 to resolve allegations it violated federal waste and community-protection laws at its phosphoric acid and fertilizer plant outside Rock Springs.

Simplot representatives signed a consent decree with the U.S. Department of Justice on July 9 in which they agreed to pay injunctive relief and civil penalties to resolve a suit brought by the federal agency.

Simplot “illegally placed” hazardous material in a waste pile of calcium sulfate byproducts known as a phosphogypsum stack system, the government claims. At...