Associations between rainfall, especially extreme rainfall, and increases in waterborne infectious disease are widely reported in the literature. Most of this research, however, has not been capable of attributing observed associations to surface hydrologic processes. Here, we leverage a rich collection of epidemiologic and environmental data from villages in rural coastal Ecuador to attribute incidence of diarrheal diseases to rainfall-runoff processes, such as pathogen concentration and dilution in rivers used for drinking water. This research represents a novel interdisciplinary epidemiologic and hydrologic effort, and evaluates a unique combination of rainfall, streamflow, and drinking water source exposures. We find that a previously observed relationship between rainfall and disease following heavy rainfall in dry periods, thought to be caused by concentration and subsequent flushing of pathogens from the land surface into surface waters, is driven by collection of drinking water from both rain and river water sources. With respect to rain water sources, this suggests a climate-driven contamination pathway separate from surface hydrologic processes. With respect to surface water sources, findings suggest that previously hypothesized concentration and dilution mechanisms do contribute to waterborne disease incidence increases and decreases, respectively. These findings demonstrate that multiple social and environmental pathways of contamination may be present and attributable to climate and hydrologic extremes, and are relevant to the development of targeted and effective interventions.