The objective of this paper was to quantitatively analyze the effect of concentrated animal feeding operations (CAFO) NPS pollution on a small watershed water quality. Monitoring was conducted from March to October, 2013. Monthly flow rate and selected water quality at each monitoring site were measured during dry days. Rainy day monitoring also was conducted. Modeling was conducted to evaluate the effect of CAFO NPS pollution on the water quality at the watershed outlet. The highest and mean concentration of selected water quality indices during rainy days were higher than those in dry days in general. The highest TN concentration measured at the CAFP pollution discharge point was 237.831 mg/L. The results revealed that the CAFO NPS pollution sources could be equally blamed for the water quality degradation of the stream. However, the effect of the NPS pollution from CAFOs seemed not to be very influential to the watershed water quality at the outlet. SWAT modeling revealed that the TN load was reduced by 18.95 %, 23.39 % and 30.53 % at the watershed outlet if the TN load at the CAFO NPS pollution discharge point reduced by 20 %, 40 % and 60 %, respectively. It was thought that the natural attenuation processes played an important role. The modeling was based only on the assumption of the load reduction and not verified by the monitored data. Therefore, it was suggested that a long term monitoring studies for the evaluation of the impact of CAFO NPS pollution on the watershed water quality be conducted.