To fully understand the impacts of the chytrid fungus Batrachochytrium dendrobatidis (Bd) on amphibians it is necessary to examine the interactions between populations and their environment. Ecologic variables can exacerbate or ameliorate Bd prevalence and infection intensity, factors that are positively related when Bd is acting on naive amphibian populations as an epidemic disease. In crawfish frogs (Lithobates areolatus), a North American species with a complex life history, we have shown that Bd acts as an endemic disease with impacts that vary seasonally; the highest infection prevalences and intensities and highest frog mortality occurred during late spring in postbreeding individuals. In this study, conducted between 28 February and 23 August 2011 in southwestern Indiana on the same population, we report an uncoupling of the previously observed relationship between Bd prevalence and intensity following an extreme drought. Specifically, there was a postdrought reduction in Bd infection intensity and mortality, but not in infection prevalence. This result suggests that the relationship between prevalence and intensity observed in Bd epidemics can be uncoupled in populations harboring endemic infections. Further, constant prevalence rates suggest either that crawfish frogs are being exposed to Bd sources independent of ambient moisture or that low-level infections below detection thresholds persist from year to year. Drought has several ecologically beneficial effects for amphibians with complex life histories, including eliminating fish and invertebrate populations that feed on larvae. To these ecologic benefits we suggest another, that drought can reduce the incidence of the severe skin disease (chytridiomycosis) due to Bd infection.