Subsurface drainage systems have been widely used to deal with soil salinization and waterlogging problems around the world. In this paper, a mathematical model was introduced to quantify the transient behavior of the groundwater table and the seepage from a subsurface drainage system. Based on the assumption of a hydrostatic pressure distribution, the model considered the pore-water flow in both the phreatic and vadose soil zones. An approximate analytical solution for the model was derived to quantify the drainage of soils which were initially water-saturated. The analytical solution was validated against laboratory experiments and a 2-D Richards equation-based model, and found to predict well the transient water seepage from the subsurface drainage system. A saturated flow-based model was also tested and found to over-predict the time required for drainage and the total water seepage by nearly one order of magnitude, in comparison with the experimental results and the present analytical solution. During drainage, a vadose zone with a significant water storage capacity developed above the phreatic surface. A considerable amount of water still remained in the vadose zone at the steady state with the water table situated at the drain bottom. Sensitivity analyses demonstrated that effects of the vadose zone were intensified with an increased thickness of capillary fringe, capillary rise and/or burying depth of drains, in terms of the required drainage time and total water seepage. The analytical solution provides guidance for assessing the capillary effects on the effectiveness and efficiency of subsurface drainage systems for combating soil salinization and waterlogging problems.