The Saemangeum watershed is required to manage water pollution effectively but the effect of liquid manure (LM) on soil and water quality in the basin is not clearly identified as yet. This study aims at assessing the effect on soil of a rice field and water quality of water bodies near the rice field during rice-crop time period to find out the effect of LM, the effect of rainfall, and the effect of rice-crop environment on soil and water quality by analyzing data of nitrogen components. As a result of the LM distribution, NO3-N was much higher than other N components in the entire soil layers and it was accelerated by rainfall right after the LM distribution. Compared to chemical fertilizer (CF), LM was slightly affected but still influenced on the surface water quality. During weak rainfall, low nitrogen concentration in topsoil was resulted as NH3-N decreased and Org-N and NO3-N increased. NO3-N concentration in the water of irrigation canals increased with time. During intensive rainfall, NO3-N and Org-N of the soil were measured highly in the submerged condition, while the water quality of the rice field was lower due to flooding into the irrigation canal as well as the growth of the rice plants. Also, total nitrogen was increased more than 7 times and it showed serious water quality deterioration due to LM and excessive fertilizer distribution, and rainfall during all rice-crop processes. The effect of LM on water quality should be studied consistently to provide critical data while considering weather condition, cropping conditions, soil characteristics, and so on.