A full-scale treatment system for swine manure was developed to eliminate discharge to surface and ground waters and contamination of soil and groundwater by nutrients and heavy metals, along with related release of ammonia, odor, and pathogens. The system greatly increased the efficiency of liquid-solid separation by polymer injection to increase solids flocculation. Nitrogen management to reduce ammonia emissions was accomplished by passing the liquid through a module where bacteria transformed ammonia into harmless nitrogen gas. Subsequent alkaline treatment of the wastewater in a phosphorus module precipitated phosphorus and killed pathogens. Treated wastewater was recycled to clean swine houses and for crop irrigation. The system was tested during one year in a 4400-head finishing farm as part of the Agreement between the Attorney General of North Carolina and swine producers Smithfield Foods, Premium Standard Farms and Frontline Farmers to replace traditional waste treatment anaerobic lagoons with environmentally superior technology. The on-farm system removed 97.6% of the suspended solids, 99.7% of BOD, 98.5% of TKN, 98.7% of soluble ammonia (NH(4)(+)-N), 95.0% of total P, 98.7% of copper and 99.0% of zinc. It also removed 97.9% of odor compounds in the liquid and reduced pathogen indicators to non-detectable levels. Based on performance obtained, it was determined that the treatment system met the Agreement's technical performance standards that define an environmentally superior technology. These findings overall showed that cleaner alternative technologies are technically and operationally feasible and that they can have significant positive impacts on the environment and the livestock industry.