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Surface runoff and infiltration are primary fecal bacteria transport mechanisms occurring in agricultural fields following manure application. The presence of macropores and biopores notably increases water infiltration, decreases surface runoff, and allows fecal bacteria and water to rapidly bypass the soil matrix during rainfall or irrigation events. This research incorporated fecal bacteria transport and biopore routines into the Root Zone Water Quality Model (RZWQM) to simulate flow and fecal bacteria transport though the soil, to subsurface drainage, and in runoff. Flow, soil fecal bacteria transport routines, and the influence of macropores and biopores on E. coli transport were evaluated based on a series of soil column experiments (28 50 85 cm) with two contrasting soil types (loamy sand and sandy loam) in which artificial, open surface connected biopores were created at two different lengths (55 cm and 65 cm). In addition, simulation of fecal bacteria transport in runoff was evaluated from a series of 2 2 m plot experiments treated with poultry litter and subjected to two rainfall storm event intensities. The new routines improved RZWQM's capability to predict rapid flow (e.g., shape of the hydrograph, time to peak, and flow breakthrough; Nash-Sutcliffe efficiency index ranged between 0.65 and 0.75 for model validation) and soil fecal bacteria transport, e.g., absolute error for the simulated event mean concentrations (EMCs) ranged between 4% and 109%. Fecal bacteria transport concentrations were underestimated in some cases, but the modified model captured the trend in concentrations observed during the soil column and plot experiments. The updated model is a simple prediction tool capable of simulating fecal bacteria transport in runoff and subsurface drainage with and without the presence of biopores.