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Component models were developed to predict ammonia nitrogen losses from cattle manure in the barn, during storage, following application, and during grazing. These relationships were integrated into a whole-farm simulation model to provide a tool for evaluating and comparing long-term nutrient losses along with other performance and economic aspects of farm production. Whole-farm simulations illustrated that the use of a free stall barn, bottom-loaded slurry storage, and direct injection of manure into the soil reduced ammonia emissions by 30-50% compared to other commonly used animal housing and manure handling systems in the northeastern US.