Bioretention can be an efficient measure of stormwater treatment. The bioretention system has been globally adapted for controlling rainfall-runoff volume and removing pollutants. However, there is a lack of systematic analysis of some hydrological processes in the bioretention facility, such as the transportation of rainfall-runoff (event water) and soil water (pre-event water). This research uniquely applied stable isotope tracing to a bioretention system to investigate the transport of rainfall-runoff and the movement of soil water in a bioretention column. The stable isotope tracing method is helpful for determining the transport process of water and is expected to enhance our understanding of bioretention systems. The ratio of the event rainfall-runoff and the pre-event soil water in the bottom outflow of bioretention columns was calculated by the stable isotope bivariate mixing model based on the oxygen and hydrogen stable isotopic data from continuous testing in the discharge of bioretention column. The time-varying proportion of event water and pre-event water in the hydrographic curve reveals that the outflow process of soil water is divided into three stages. In the early stage, all the outflow was soil water, accounting for about 6–13% of the total outflow. In the middle stage, the proportion of soil water rapidly decreased from 100% to 20% within a few minutes. In the later stage, the soil water proportion decreased slowly from 20% to 0%. The outflow of soil water accounted for more than 36% of the total outflow and decreased with the extension of the drought period. Soil water is a critical part of the bottom outflow of bioretention columns, and the influence of soil water on the hydrological effect of bioretention columns cannot be ignored.