Four actual cultivations were prepared and a variety of soybean was cultivated. A H-flume, an automatic water level gauge and an automatic water sampler were installed at the outlet of each plot equipped for the measurement of flow rate and its water quality. The amount of rainfall of the study area in 2013 was measured as 975.6 mm which was much lower than the annual average rainfall of 1,271.8 mm, resulting in less occurrences in rainfall-runoff events. Rainfall-runoff events were occurred three times during the rainfall event of 4~5 July, 23 and 24 August. The characteristics of NPS pollution discharge of the plots and the reduction effect of the selected BMPs were analyzed during these events. The reduction effect of straw mat and soil amendments (Polyacrylamide (PAM) and Gypsum) on runoff ratio ranged between 38.2 and 92.9% (average 71.6%). The NPS pollution load reduced between 27.7 and 95.1% (average 70.0%) by the application of rice straw mat and soil conditioner when compared with that of control plot. Soybean yield (2,133.3 kg/ha) of the straw mat covered plots increased by 14.3% when compared with control (1,866.7 kg/ha). The effect of straw mat on the yield was not economically viable if the material and accompanying labor costs were considered. The data collected and analyzed on different soil textures and crops in this study are expected to be a fundamental reference for the expansion of the results to the application nationwide and the development of NPS pollution management policies.