Increasing the water use efficiency of crops is an important agricultural goal closely related to the root system —the primary plant organ for water and nutrient acquisition. In an attempt to evaluate the response of root growth and development of soybean to water supply levels, 200 genotypes were grown in a sandy field for 3 years under irrigated and non-irrigated conditions, and 14 root traits together with shoot fresh weight and plant height were investigated. Three-way ANOVA revealed a significant effect of treatments and years on growth of plants, accounting for more than 80% of the total variability. The response of roots to irrigation was consistent over the years as most root traits were improved by irrigation. However, the actual values varied between years because the growth of plants was largely affected by the field microclimatic conditions (i.e., temperature, sunshine duration, and precipitation). Therefore, the best linear unbiased prediction values for each trait were calculated using the original data. Principal component analysis showed that most traits contributed to principal component (PC) 1, whereas average diameter, the ratio of thin and medium thickness root length to total root length contributed to PC2. Subsequently, we focused on selecting genotypes that exhibited significant improvements in root traits under irrigation than under non-irrigated conditions using the increment (I-index) and relative increment (RI-index) indices calculated for all traits. Finally, we screened for genotypes with high stability and root growth over the 3 years using the multi-trait selection index (MTSI).Six genotypes namely, GmJMC130, GmWMC178, GmJMC092, GmJMC068, GmWMC075, and GmJMC081 from the top 10% of genotypes scoring MTSI less than the selection threshold of 7.04 and 4.11 under irrigated and non-irrigated conditions, respectively, were selected. The selected genotypes have great potential for breeding cultivars with improved water usage abilities, meeting the goal of water-saving agriculture.