The aquatic pathogen Batrachochytrium dendrobatidis (Bd) can cause declines in amphibian populations and species extinctions worldwide. In tadpoles, epizootic events have not been reported; however, there is a possibility for rapid spread of disease in water. Here, we quantified Bd infection dynamics in tadpoles from two streams in the northeastern Atlantic forest of Brazil. Bd prevalence varied seasonally and increased during the rainy season. Aplastodiscus sibilatus and Proceratophrys renalis tadpoles were Bd positive in both seasons, whereas Agalychnis granulosa tadpoles were Bd positive only during the rainy season. Bd prevalence was higher in A. sibilatus than in A. granulosa and P. renalis. We found that larger individuals have a higher probability of being Bd positive, independent of the developmental stage. Moreover, we found that canopy cover, water flow, water temperature, water depth, and pH were associated with Bd prevalence. Our results highlight the fact that tadpoles can serve as pathogen reservoirs; therefore, monitoring anuran larvae populations in these habitats can enhance the impact assessment of this pathogen in biodiversity hot spots.