Crop production in rice paddy fields is of great importance because of declining rice consumption and the low self-sufficiency ratio for field crops in Korea. A controlled drainage system (CDS) is recognized as an effective means to adjust water table (WT) levels as needed and control soil water content to improve the soil environment for optimum crop growth. The present study evaluated the effects of a CDS on soil characteristics, including soil water distribution and soybean development in paddy fields. The CDS was installed with two drain spacing (3 m and 6 m) at the experimental paddy field at the National Institute of Crop Science, Miryang, Korea. It was managed with two WT levels (0.3 m and 0.6 m) during the growing season. Soil water content, electrical conductivity and plant available nitrogen content in the soil were significantly greater in the 0.3 m WT management plots than in the 0.6 m plot and the control. At the vegetative stage, chlorophyll content was significantly lower with higher WT control because of excess soil moisture, but it recovered after the flowering stage. Soybean yield increased with WT management and the 0.6 m WT treatment produced the greatest grain yield, 3.38 ton ha-1, which was 50% greater than that of the control. The CDS directly influenced outflow through the drains, which significantly delayed nutrient loss. The results of this study indicated that WT management by CDS can influence soil characteristics and it is an important practice for high yielding soybean production in paddy fields, which should be considered the crop growth stages for stable crop production.