Vegetative buffer strips (VBS) are a common best management practice to improve the microbial quality of surface runoff.   However, wide variations in the removal efficiency of VBS for microorganisms have been reported in the literature.   Some of these reported variations are likely due to our incomplete understanding of microorganism exchange and retention processes in the VBS and soil.   To overcome some of these limitations, the COMSOL software package was used to simulate water flow and pathogen transport in overland flow and in variably saturated soils under a wide range of conditions.   Specifically, we conducted numerical experiments to examine: (1) the influence of the surface mixing zone, spatial variations in surface topography, and depression storage on pathogen removal; (2) the dynamic interactions of surface and subsurface water flow on pathogen transport; (3) the influence of pathogen size; and (4) and the role of pathogen retention parameters.   Results reveal that the performance of VBS on pathogen removal from surface water is controlled by exchange with the soil which is a function of soil texture and structure, and surface topography.   Removal of pathogens in runoff water by VBS can be optimized by selection and/or modification of soil properties and surface topography to enhance exchange with the soil.