The scale of influence of hydrological and thermal conditions on plant disease remains uncertain for most natural plant pathosystems, restricting our ability to predict the potential impacts of climate change. Analysis of the spatiotemporal spread of a fungal rust pathogen across four naturally occurring flax populations over the course of five growing seasons reveals both expected relationships with snow cover, relative humidity and temperature, and a novel footprint of severe drought. This indicates that climate change may have substantial drought-mediated impacts on the spread of plant disease, and points to a need for further research integrating population-level epidemiological studies with mechanistic environmental studies to explore the effects of drought on natural plant epidemics.