This study analyzed runoff characteristics of non-point sources pollutant and evaluated removal of pollution by BMP(Best Management Practice) using BASINS/WinHSPF model. Hourly meterological data including input data was provided from 2010 to 2011 year to run HSPF model in Miho stream watershed. As the results of calibration and validation of the model, the model could be successfully performed to simulate the flow and water quality parameters. The apprehensive area of non-point source pollution was chosen by non-point source pollution per area of a tributary to the Miho stream and applied constructed wetland in area chosen. Three scenarios were based on installation area of an constructed wetland and HSPF model would be applied to estimate the pollutant removals through the constructed wetland. The removal rates of pollutants through the constructed wetland were estimated with the runoff and water quality parameters by the comparisons of before and after the constructed wetland application.