Batrachochytrium dendrobatidis (Bd), a fungal pathogen that causes amphibian chytridiomycosis, has been implicated in population declines globally. To better understand how Bd affects survival and how threats vary spatially and temporally, we conducted long-term (range: 9–13 yrs) capture-recapture studies of boreal toads (Anaxyrus boreas) from three similar communities in western Montana. We also estimated temporal and spatial variation in population-level Bd prevalence among populations and the potential role of co-occurring Columbia spotted frogs (Rana luteiventris) in driving infection dynamics. Hierarchical models that accounted for detection uncertainty revealed Bd reduced apparent survival in one population that declined, was unassociated with survival in one stationary population, and was associated with increased survival in one population that is near extirpation. Despite different effects of Bd on hosts, pathogen prevalence was similar and synchronous across the populations separated by 111–176 km. Variation in Bd prevalence was driven partly by seasonal temperatures, but opposite the direction expected. Bd prevalence also decreased sharply over time across all populations, unrelated to trends in temperature, boreal toad survival, or infection dynamics of co-occurring Columbia spotted frogs. Toad Bd prevalence increased when frog abundance was high, consistent with an amplification effect. However, Bd prevalence of toads decreased as Bd prevalence of spotted frogs increased, consistent with a dilution effect. Our results reveal surprising variation in responses to Bd and show pathogen prevalence is not predictive of survival or population risk, and they illustrate the complexity in understanding disease dynamics across multiple populations.