Consolidation changes the geotechnical properties of a cutoff wall with depth. However, current research in transport theory fails to account for this factor. In this paper, a model for two-dimensional transport of degradable organic contaminants in a buffer layer-cutoff wall-aquifer system is developed, which takes the impacts of consolidation behavior into account for the first time. The finite-difference approach is employed to address this model, and its reasonableness is exhibited by the comparative analyses of three-different scenarios. Following this, a case-study on the barrier performance shows that accounting for the cutoff wall’s consolidation behavior prolongs the defined breakthrough time tb compared to when it is neglected. When a change in the cutoff wall consolidation parameter increases the horizontal and vertical effective stresses, its anti-fouling effectiveness is enhanced. Moreover, reducing the depth of the maximum inflow boundary concentration and increasing the concentration distribution range result in a decrease in tb. When the degradation half-life ≤ 400 years, the degradation effect should be considered to provide an accurate assessment of the cutoff wall’s longevity. For the “enclosure” cutoff walls, the appropriate thicknesses of the buffer layer and the cutoff wall can be determined based on the site environment and the construction cost.