North America's protected lands harbor biodiversity and provide habitats where species threatened by a variety of stressors in other environments can thrive. Yet disease, climate change, and other threats are not limited by land management boundaries and can interact with conditions within protected landscapes to affect sensitive populations. We examined the population dynamics of a boreal toad (Anaxyrus boreas boreas) metapopulation at a wildlife refuge in northwestern Montana, USA, over a 16‐year period (2003–2018). We used robust design capture‐recapture models to estimate male population size, recruitment, and apparent survival over time and in relation to the amphibian chytrid fungus (Batrachochytrium dendrobatidis). We estimated female population size in years with sufficient captures. Finally, we examined trends in male and female toad body size and condition. We found no evidence of an effect of disease or time on male toad survival but detected a strong negative trend in recruitment of new males to the population. Estimates of male and female abundance decreased over time. Body size of males and females was inversely related to estimated population size, consistent with reduced recruitment to replace adults, but body condition of adult males was only weakly associated with abundance. Together, these results describe the demography of a near‐extirpation event, and point to dramatic decreases in the recruitment of new individuals to the breeding population as the cause of this decline. We surmise that processes related to the restoration of historical hydrology within the refuge adversely affected amphibian breeding habitat, and that these changes interacted with disease, life history, and other factors to restrict the recruitment of new individuals to the breeding population over time. Our results point to challenges in understanding and predicting factors that influence population change and highlight that current metrics for assessing population status can have limited predictive ability. Published 2021. This article is a U.S. Government work and is in the public domain in the USA.