Pathogen-host systems become complex when they involve life histories with multiple stages. Understanding these complexities is particularly important for investigating the infection dynamics of the amphibian pathogen Batrachochytrium dendrobatidis (Bd). Here, we investigate whether Bd infection susceptibility differs between host life stages and determine the influence of environmental factors on Bd infection rates across remnant populations of a Neotropical torrent frog. We found that Bd infection probability varies between tadpoles and adults in Hylodes phyllodes, with tadpoles exhibiting a higher likelihood of infection. Tadpoles are tolerant to Bd, acting as zoospore reservoirs, potentially aiding in the pathogen's persistence in the environment and infecting other susceptible hosts. Topographic complexity, species richness, the human footprint, precipitation seasonality and diurnal temperature variations influenced Bd infection rates. Conservation strategies should encompass both host life stages, monitoring from larvae to adults, while also evaluating threats synergistically, such as the human footprint, to effectively predict and mitigate the impact of Bd on susceptible populations.