Livestock operations have been highly intensified over the last decades, resulting in the advent of large concentrated animal feeding operations (CAFOs). Intensification decreases production costs but also leads to substantial environmental impacts. Specifically, nutrient runoff from livestock waste results in eutrophication, harmful algal blooms, and hypoxia. The implementation of nutrient recovery systems in CAFOs can abate nutrient releases and negative ecosystem responses, although they might negatively affect the economic performance of CAFOs. We design and analyze potential incentive policies for the deployment of phosphorus recovery technologies at CAFOs considering the geospatial vulnerability to nutrient pollution. The case study demonstration consists of 2217 CAFOs in the U.S. Great Lakes area. The results reveal that phosphorus recovery is more economically viable in the largest CAFOs due to economies of scale, although they also represent the largest eutrophication threats. For small and medium-scale CAFOs, phosphorus credits progressively improve the profitability of nutrient management systems. The integration of biogas production does not improve the economic performance of phosphorus recovery systems at most of CAFOs, as they lack enough size to be cost-effective. Phosphorus recovery proves to be economically beneficial by comparing the net costs of nutrient management systems with the negative economic impact derived from phosphorus releases. The incentives necessary for avoiding up to 20.7×103 ton/year phosphorus releases and achieve economic neutrality in the Great Lakes area are estimated at $223 million/year. Additionally, the fair distribution of limited incentives is studied using a Nash allocation scheme, determining the break-even point for allocating monetary resources.