Fungal disease has important effects in natural and agricultural plant populations; however, we are still uncovering factors that influence severity in these systems. Understanding these factors is especially important because it has been predicted that climate change will increase fungal disease widely as a result of changes in precipitation. Here, we investigate the role of water availability and other ecological variables in determining disease severity of a foliar fungal disease. For this study, we focused on natural populations of an important annual, herbaceous plant, Brassica rapa and its fungal disease, Alternaria blackspot. We explored three hypotheses: (1) The factors that drive disease severity differ early in the growing season compared to late in the growing season. (2) Disease severity patterns for this fungus are driven by water availability to a greater extent than other ecological variables. (3) Disease severity increases with plant density. To address these hypotheses, data were collected in a spatially structured manner at two time points during the summer of 2011 from four B. rapa plant populations along the California and Oregon coasts. We found no clear factors drove disease severity early in the growing season, while factors such as host density, herbivory, sun exposure, and host developmental stage influenced disease severity later in the season. We found that soil moisture did not have a clear relationship with disease severity, and that greater host density supported greater disease severity. Our findings suggest that there are many factors influencing fungal disease, and the effects of these factors vary over the course of the growing season. These results have important implications for monitoring and predicting the effects of climate change on plant disease.