The research presented in this paper focuses on the application of a newly developed physically based watershed modeling approach, which is called representative elementary watershed approach. The study stressed the effects of uncertainty of input parameters on the watershed responses (i.e., simulated discharges). The approach was applied to the Zwalm catchment, which is an agriculture-dominated watershed with a drainage area of 114 km2 located in East Flanders, Belgium. Uncertainty analysis of the model parameters is limited to the saturated hydraulic conductivity because of its high influence on the watershed hydrologic behavior and availability of the data. The assessment of output uncertainty is performed using the Monte Carlo method. The ensemble statistical watershed responses and their uncertainties are calculated and compared with measurements. The results show that the measured discharges fall within the 95% confidence interval of the modeled discharge. This provides the uncertainty bounds of the discharges that account for the uncertainty in saturated hydraulic conductivity. The methodology can be extended to address other uncertain parameters as far as the probability density function of the parameter is defined.