The occurrence of pathogen bacteria in surface waters threatens the world population health. In particular, fecal contamination of surface waters have been issued in developing countries such Lao P.D.R. where surface water is highly contaminated with pathogens of fecal origin due to the lack of adequate sanitation systems. However, the environmental fate and transport of Fecal Indicator Bacteria (FIB) is still poorly known in tropical areas, including LAO P.D.R. In this study, observations on bacterial water quality and flow rates in a 60-ha atchment in Northern Laos were used to explore the watershed-scale fate and transport of FIB Escherichia coli (E.coli) by using the Soil and Water Assessment Tool (SWAT), wherein the influences of the bacterial regrowth, deposition, resuspension, and hyporheic exchange on FIB level were explored. This study applied three different modules to simulate E.coli concentration in stream: 1) original SWAT b acteria module which considers a die-off process only, 2) modified SWAT bacteria module by adding sediment resuspension and deposition, and 3) modified SWAT bacteria module with bacterial regrowth/hyporheic exchange. The results demonstrated that the hyporheic ex change of bacteria across the Sediment-Water Interface (SWI) should be considered to simulate FIB concentration not only during wet weather, but also during the dry season, or base flow period. However, the regrowth process could not simulate FIB concentration throughout the year and can only simulate the wet and dry seasons separately.