North Carolina is the second largest producer of swine in the United States where concentrated animal feeding operations provide economic benefits with significant environmental risks. Unfortunately, North Carolina ranks among the highest in the nation in vulnerability to manure nutrient contamination based on soil runoff potential, soil percolation, erosion, and land application of treated waste. Thus, the state is especially vulnerable to the ecological impacts associated with industrialized agriculture. Environmental risks associated with swine factory farms includes accidental breeches of hog waste lagoons and chronic effects associated with unregulated pollution through the atmosphere and groundwater. Many farms are located in regions susceptible to flooding, which increases risk of both negative ecological impacts and economic losses due to flooding caused by frequent hurricanes which impact the state. Chronic and acute contamination events associated with swine production impacts all uses of receiving rivers and coastal zones. Eutrophication of waterways contributes to low dissolved oxygen levels, algal blooms, growth of toxic dinoflagellates, and large fish kill events. This case study examines the environmental risks associated with animal feeding operations, examines current governance methods, and suggests possible solutions to prevent the deleterious effects of swine waste management on the integrity of freshwater habitats.