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This research examined the relationship between animal agriculture and watershed impairment in South Carolina from a GIS-based spatial, empirical approach. Animal agriculture was represented by cattle, poultry and swine operations that were measured in terms of animal population, farms, facilities and units as well as their derived density variables. Watershed impairment was measured in terms of priority ranks for dissolved oxygen (DO), fecal coliform (FC) bacteria, phosphorus (P), and pH problems. The 11-digit hydrological units of watersheds were used as the units of analysis. Map overlay, spatial summarization, canonical correlation, multiple regression, and Pearson correlation were performed to determine how strong the relationships are, which animals have larger impacts, and where the problem areas are. The results indicate that there are only very weak, though statistically significant, associations between animal agriculture and watershed impairment in this state. FC bacteria are the most widely spread problem and cattle facilities appear to have slightly larger impacts on watershed quality than poultry farms do whereas swine do not aggravate the existing impairment. State policies on animal regulations and environmental standards should acknowledge these differences among impairment types, animal operations, and geographic regions. While cattle feeding operations should be targeted for further research and reduction of animal related pollution particularly in the identified problem areas, more resources should be used in the identification and control of non-animal agricultural sources that are the major causes of DO, FC, P and pH related impairment in the state of South Carolina.