Background: Field crop production at paddy field is great concern due to the declining of rice consumption and low crop self-sufficiency ratio in Korea. Groundwater management system will make optimal soil conditions and crop growth possible. The present study was evaluated the effect of groundwater management practice on soil characteristics including soil water distribution and soybean growth at paddy field. Methods: Groundwater management system was installed with two drain spacing (3m & 6m) at silt loam field at the experimental station in National Institute of Crop Science, Korea. It was managed with two ground water level (0.3m & 0.6m) during the growing season. Results: The depth of groundwater table was significantly influenced on drainage amount from the soil profile through the drains. Soil water content, electrical conductivity and plant available nitrogen content in soil was significantly greater with 0.3m water table management plot compared to 0.6m plot and the control. At the vegetative stage chlorophyll concentration was significantly lower with higher water table control, but it was recovered at the post-flowering stage. Soybean yield was increased with groundwater management system and soybean yield with 6M drain spacing and 0.6m water table level was 3.38 ton/ha, which was 50% greater compared to the control. Discussions: Groundwater management system directly influenced on drainage amounts, which significantly delayed the infiltration rate and nutrient loss. These results are comparable to other researches, which reported that the reductions of drain flow and nutrient loss are the major mechanism to better crop development. Conclusion: The results of this study indicate that groundwater management system can influence on soil characteristics and it is an important practice of high yielding soybean production at paddy field, which should be considered crop development stages for stable crop production.