As much as 1.4 billion tons of manure is produced yearly in the U.S., which is primarily used for crop production. This poses a significant risk to human and environmental health as manure is a major source of antibiotic resistance genes (ARGs) and per- and polyfluoroalkyl substances (PFAS) input to the environment. This project will leverage our multidisciplinary team’s expertise in environmental microbiology, resource recovery, and analytical chemistry to comprehensively evaluate the occurrence of ARGs and PFAS in manure vs. various fertilizer alternatives, and in runoff water from farms implementing these manure management practices. Successful completion of this project will guide improved runoff management by informing the efficacy and effectiveness of converting manure to fertilizer alternatives in mitigating two groups of emerging contaminants. This project will also support the dairy industry, the largest single segment of New York’s agricultural industry, by unveiling additional environmental benefits of converting manure to fertilizer alternatives for cropland application.