This dataset includes data used to summarize trends and identify best-fit models to explain patterns in presence-absence and abundance of Pseudogymnoascus destructans (Pd) in environmental substrates and on bats within six bat hibernacula at different stages of white-nose syndrome (WNS). Data relating to environmental substrates include: dates and relative spatial locations of samples collected within study hibernacula, presence and quantity of Pd in samples based on qPCR analysis, and daily temperature parameters at each sample location on the days samples were collected. Data relating to bats include: dates and relative spatial locations of hibernating bats that were sampled, species, sex, weight(g), forearm length(mm), body mass index (weight/forearm), proportion of the wing with visible fungus or fluorescence characteristic of WNS under hand-held UVA light and presence and quantity of Pd in wing-skin swab samples based on qPCR analysis. Measures of time since first detection of WNS at each study hibernaculum are also included in the dataset.