This study aimed to evaluate the nutrient load balance from rice paddy fields with different topographies, alluvial plain and local valley. Continuous monitoring from May to September, 2013 was conducted for water quantification and qualification from alluvial plain in Yeoju region (32 ha) and local valley in Jincheon region (24 ha). The discharge rates of T-N from the alluvial plain were 57.2, 5.84, 22.7, and $5.20kg\;ha^{-1}$ for irrigation, precipitation, drainage, and percolation, respectively. In case of local valley, T-N loads were 34.6, 4.73, 21.1, and $4.15kg\;ha^{-1}$ for irrigation, precipitation, drainage, and percolation, respectively. In contrary, the T-P loads from the alluvial plain were 2.23, 2.22, 2.54, and $0.41kg\;ha^{-1}$ for irrigation, precipitation, drainage, and percolation, respectively. In case of local valley, T-P loads were 1.44, 1.57, 1.82, and $0.34kg\;ha^{-1}$ for irrigation, precipitation, drainage, and percolation, respectively. The nutrient contents in drainage water were influenced by the amount of waters, rainfall, and surface drainage water. The Pearson correlation analysis showed that rainfall was significantly correlated with nutrient loads from July to August due to the amount of runoff in local valley paddy field, and irrigation was related with nutrient loads of drainage from July to August. This study showed that paddy rice farming in alluvial plain and local valley might be beneficial to water quality protection.