<p>There is a need to study water and nutrient transport system of a watershed in order to find effective measurements to reduce amount of non point source pollutant loads. Our research uses WEP model to simulate water and nutrient transport system of Koise watershed. Data of land covers, meteorology, rivers’ properties, fertilizer input, nitrate concentration in rainfall and others of Koise watershed was processed as inputs to WEP model. Hydrograph and inorganic nitrogen cycle of year 2007 were simulated. Simulation result pattern of year 2007 agrees well with occasional observed data and estimation from ANN model. Year 2008 hydrograph was simulated by the same set of parameter for verification purpose. High reproducibility rate of 0.98 and 0.91 is achieved. Sensitivity of uncertain parameters was analyzed in search of better parameter set to reduce simulation error. Discharge amount of pollutant loads is found to be hugely influenced by fertilizer input, nitrate concentration in rainfall and underground water.</p>