The scale of influence of hydrological and thermal conditions on disease remains uncertain for most wild plant pathosystems, thus restricting our ability to predict the impacts of climate change. Analysis of the spatiotemporal spread of a fungal rust pathogen throughout four naturally occurring flax populations over the course of five growing seasons reveals relationships between epidemic magnitude and snow cover, relative humidity and temperature, as well as an unexpectedly significant effect of severe drought on disease progression. These results indicate that climate change will likely disrupt wild plant epidemics, and points to a need for further epidemiological studies characterizing the effects of environmental conditions on population‐level disease dynamics in natural pathosystems.