Drought tolerance research using large plant populations may benefit from high-throughput phenotyping systems which allow for accurate measurement of daily single-plant water use. In this work, we identify and optimize a soil mix as part of a passive, bottom-watered pot culture system for soybean (Glycine max (L.) Merr.), which can induce varying but consistent levels of drought stress via adjustment of pot-specific water tables. The soil media within the pot wicks water upwards to maintain soil moisture equilibrium through the rooting column over an entire growth cycle, even as the roots take up water. Plants remained healthy throughout the growth cycle and treatments produce significant differences in water use, growth and yield traits. This system can also be adapted to large-population phenotypic screenings, including Genome-Wide Association Studies. Such a system would greatly improve the feasibility of measuring growth and yield traits in large plant populations grown to maturity.