Concentrated animal feeding operations (AFO) and many AFO are required to comply with state and federal environmental regulations specifically related to the protection of water quality. Most regulations are based on the need to account for and control nutrient flow on-farm to minimize buildup, leaching, and runoff of nutrients that may pose a risk to surface and ground water quality. Attempts to encourage the control of nutrient flow include the requirements for comprehensive nutrient management plans (CNMP), conservation practice plans, storm water pollution prevention plans, animal mortality management, and emergency action plans. The overall goal of the CNMP on a livestock and poultry farm is to sustain a whole farm nutrient mass balance. An extensive auditing and assessment program evaluates the status of nutrient management on-farm and develops an action plan to minimize water pollution. An annual audit and review checks the performance of the concentrated AFO and AFO on environmental stewardship and identifies areas needing improvement. Critical control points that need to be audited and assessed are 1) nutrients imported on-farm, 2) nutrients exported off-farm, 3) nutrient status of soils and water, 4) manure handling and storage facilities, 5) conservation practices, 6) runoff waste water control, 7) land application practices, 8) animal mortality practices, 9) record keeping system, 10) operation and maintenance plan, and 11) alternative treatment systems, if applicable. Professional animal scientists can contribute significantly to livestock and poultry producers by providing assessments and audits of nutrient management along with other qualified professionals in the development of CNMP.