<p>Underground structures have been shown to have a great influence on groundwater seepage in urban aquifers, yet few studies explore the influence of seepage channels at the soil-structure interface on groundwater seepage, particularly in multi-aquifer-aquitard systems. A simplified laboratory test consisting of multi-aquifer-aquitard was conducted to study the potential influence of seepage channels on groundwater seepage. The seepage law and the soil deformation law were investigated as increasing numbers of seepage channels. A numerical model is employed to verify the laboratory test results, in which a multi-aquifer-aquitard model was established, considering the permeability and number of seepage channels at the soil-structure interface. Results indicate that seepage erosion channels impact not only the pore pressure in confined aquifers but also the soil deformations. During upward seepage, aquifer pore water pressure presents phased changes that include steep increase stages and smooth increase stages, and soil layer settlement follows a similar pattern. Increased seepage channels’ number and permeability lead to pore water pressure dissipation in confined aquifers, causing soil compression and surface subsidence. Meanwhile, this effect is also limited by the number of seepage channels and permeability. The impact can be minimal when the permeability and number of channels are very small. This phenomenon is explained by the hydraulic connection effect (HCE) between aquifers due to seepage channels, which may be another potential reason for land subsidence.</p>