Concentrated Animal Feeding Operations (CAFOs) are large-scale farms that cause significant environmental degradation and contamination through the discharge of their waste. National Pollutant Discharge Elimination System, or NPDES, permits are one way that states set their own standards for CAFOs; the permits regulate the wastewater and manure discharged by CAFOs. The level of stringency for these NPDES permits varies by state. This paper analyzes typical case studies of the NPDES permitting process in two different states, Michigan and Illinois, and the agencies each state employs for its CAFO regulations. It finds that the NPDES permitting process in Michigan and Illinois are similar in structure, however Michigan’s permits themselves implement stricter environmental protections and take a longer timeline to be approved. With its stricter standards, Michigan’s regulatory agency has faced stronger pushback from farmers while Illinois’s looser regulations have lended themselves to a collaborative relationship with the state’s Farm Bureau. These findings have implications in the way regulations can influence the relationship between regulatory agencies and their respective industries.