1. Fungal diseases are an emerging global problem affecting human health, food security and biodiversity. Ability of many fungal pathogens to persist within environmental reservoirs can increase extinction risks for host species and presents challenges for disease control. Understanding factors that regulate pathogen spread and persistence in these reservoirs is critical for effective disease management. 2. White-nose syndrome (WNS) is a disease of hibernating bats caused byPseudogymnoascus destructans(Pd), a fungus that establishes persistent environmental reservoirs within bat hibernacula, which contribute to seasonal disease transmission dynamics in bats. However, host and environmental factors influencing distribution ofPdwithin these reservoirs are unknown. 3. We used model selection on longitudinally collected field data to test multiple hypotheses describing presence-absence and abundance ofPdin environmental substrates and on bats within hibernacula at different stages of WNS. 4. First detection ofPdin the environment lagged up to one year after first detection on bats within that hibernaculum. Once detected, the probability of detectingPdwithin environmental samples from a hibernaculum increased over time and was higher in sediment compared to wall surfaces. Temperature had marginal effects on the distribution ofPd. For bats, prevalence and abundance ofPdwere highest onMyotis lucifugusand on bats with visible signs of WNS. 5.Synthesis and applications. Our results indicate that distribution ofPseudogymnoascus destructans(Pd) within a hibernaculum is driven primarily by bats with delayed establishment of environmental reservoirs. Thus, collection of samples fromMyotis lucifugus, or from sediment if bats cannot be sampled, should be prioritized to improve detection probabilities forPdsurveillance. Long-term persistence ofPdin sediment suggests that disease management for white-nose syndrome should address risks of sustained transmission from environmental reservoirs.