Excess nutrient runoff can profoundly alter aquatic habitats and has been associated with changes in host–pathogen interactions. Floating macrophyte mats have been suggested as a management strategy to improve water quality for aquatic communities and, thus, may have the potential to protect hosts from some disease outbreaks. We assessed the impact of ammonium nitrate and sodium phosphate addition in the presence or absence of floating macrophyte mats (blue flag iris [Iris versicolor] and ice dance sedge [Carex morrowii]) on Cope's Gray Treefrog (Hyla chrysoscelis) metamorphosis to examine whether macrophyte management treatments improve outcomes for amphibians. At metamorphosis, we infected individuals with the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd), to assess whether larval treatments resulted in differential susceptibility to this pathogen. We found that nutrient addition significantly increased time to metamorphosis without affecting mass at metamorphosis or survival. Additionally, Bd exposure decreased mass of juvenile treefrogs, regardless of earlier larval environment or condition at metamorphosis. Macrophyte addition had no direct impact on larval anurans, but the aquatic community was altered via fluctuations in aquatic nutrient concentrations. Overall, our study suggests that nutrient exposure and Bd infection individually affect anurans, and larval exposure to nutrients may have latent effects on metamorphosed anurans that could affect future fitness.