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Agricultural practices have a profound impact on watershed dynamics, water quality, and the well-being of aquatic life. One major concern is agricultural pollution, particularly the excess of nutrients, which can elevate disease risks in various host-pathogen relationships. However, the exact mechanisms driving this effect remain uncertain. Elevated nutrient levels are believed to significantly influence populations of aquatic environmental bacteria, potentially reshaping the microbiomes of aquatic organisms and affecting their vulnerability to disease. Despite this, the impact of nutrient enrichment on host microbiomes as a link to diseases in aquatic organisms has been largely overlooked. In this study, we investigated the impact of nutrient enrichment on the skin-associated microbial communities of the American bullfrogLithobates catesbeianus. We observed a significant shift in bacterial richness and community composition in nutrient-enriched ponds compared with reference ponds. Although the proportion of the community inhibitory towardsBatrachochytrium dendrobatidis(Bd) did not change significantly,Bdloads were markedly higher in nutrient-enriched ponds. Nutrient enrichment significantly altered carbon utilization patterns as measured by Biolog EcoPlates, and antibiotic resistance was prevalent across all ponds and samples, with resistance to trimethoprim, sulfamethazine, and chloramphenicol significantly higher in nutrient-enriched ponds. Our findings indicate that nutrient enrichment affects the structure and function of skin-associated microbial communities in American bullfrogs, influencing bothBdload and antibiotic resistance.