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Managing the environmental risk associated with livestock production is a significant challenge. Nitrogen and phosphorus are commonly implicated as the sources of ground and surface water quality problems associated with livestock production. The degree of imbalance between these nutrient inputs and the managed nutrient outputs for a livestock operation defines the magnitude of potential environmental risk and provides insight as to the underlying causes of these challenges. A nitrogen and phosphorus balance was constructed for 33 Nebraska confinement livestock operations. Twenty-five and 17 of these operations experienced significant nitrogen and phosphorus imbalances, respectively (50% more nutrient inputs than outputs). Nutrient inputs on many livestock operations were observed to be two to four times greater than nutrient outputs as managed crop and livestock products. Size of the livestock operation and the degree of integration of livestock with a cropping operation provided only limited explanation of the variation in nutrient balance observed among the individual operations. Management options that contribute to a more favorable nutrient balance were also identified. Management decisions related to feeding program and exporting of manure nutrients to off-farm users were observed to have a substantial impact on the nutrient imbalance. For modern livestock production systems to successfully respond to nutrient-related environmental problems, management strategies must be implemented that address the commonly experienced imbalances of nitrogen and phosphorus.