This Note challenges the Alt court’s restriction of the EPA’s authority to regulate Concentrated Animal Feeding Operations (CAFOs) and proposes that the EPA conduct a new rulemaking to address this issue. CAFOs pollute our nation’s waterways with contaminated manure, damaging our environment and injuring public health. Recognizing their potential to pollute, Congress included CAFOs within the statutory definition of a point source in the Clean Water Act in 1972. Fifteen years later, Congress amended the statute and exempted agricultural stormwater from the definition of a point source. Controversy surrounded the application of the agricultural stormwater exemption to CAFOs until 2003, when the EPA specified that the exemption only applied to precipitation-based discharges from the land application area of a CAFO when manure had been applied pursuant to prudent agricultural practices. Unfortunately, in Alt v. EPA, industry capitalized on the ambiguity in the Clean Water Act and secured a district court ruling expanding the agricultural stormwater exemption to include discharges outside the land application area, allowing CAFOs to further pollute our waterways. After providing the relevant history of CAFO regulation, this Note critiques the Alt decision—concluding that the court misinterpreted the agricultural stormwater exemption. Finally, it argues that the EPA should initiate a rulemaking and comprehensively define the agricultural stormwater exemption to prevent further environmental degradation and harm to human health.