Bacterial pathogens in surface waters threaten human health. The health risk is especially high in developing countries where sanitation systems are often lacking or deficient. Considering twelve flash-flood events sampled from 2011 to 2015 at the Houay Pano catchment, and using Escherichia coli as a fecal indicator bacteria, our objective was to quantify the contributions of both surface runoff and sub-surface flow to the in-stream concentration of E. coli during flood events. We found that in-stream E. coli concentration is high regardless of the contributions of both surface runoff and sub-surface flow to the flood event. However, we measured the highest concentration of E. coli during the flood events that are predominantly driven by surface runoff. This indicates that surface runoff, and causatively soil surface erosion, are the primary drivers of in-stream E. coli contamination. This was further confirmed by the three models applied to each flood event (linear model, partial least square model, and mixing model). The three models showed that the percentage of surface runoff in stream flow was the best predictor of the flood event mean E. coli concentration. The mixing model yielded a Nash-Sutcliffe efficiency of 0.65 and showed that on average, 89% of the in-stream concentration of E. coli resulted from surface runoff, while the overall contribution of surface runoff to the stream flow was 41%.