The effect of geometric imperfections in both diameter and position of jet-grouted columns on the watertightness of an underground cement-treated slab is investigated in this study. A three-dimensional discretized algorithm is proposed to facilitate the detection and measurement of untreated zones that penetrate the treated slab. The normalized flow rate of a cement-treated slab is then evaluated by calculating the harmonic average area of the penetrated defect. Statistical evaluation of the gross flow rate through the penetrated defects is carried out via Monte Carlo simulations. The results show that a more economic design is obtainable if intracolumn variation of diameter is considered or multi-shaft jet-grouting is used. Based on the statistical results, a reliability-based design method is proposed for designers to strike a balance among various design parameters, including slab thickness, depth, column diameter, and column spacing.