Physical barriers are widely used to control seawater intrusion (SWI). Amongst different kinds of physical barriers, mixed physical barriers (MPBs) are shown to be an effective approach to prevent SWI. However, the system may hinder the discharge of fresh groundwater and the removal of residual saltwater trapped in the inland aquifers of MPBs. Herein, using the validated numerical model, for the first time, we investigated the dynamics of residual saltwater and groundwater discharge after the installation of MPBs. For examining the applicability of MPB and its response to structural variations and hydraulic gradient, the comparison with traditional physical barriers and sensitivity analysis was also carried out. The MPB increased the mixing area of freshwater and saltwater at the beginning of the removal process, resulting in the reduction of the saltwater wedge length (R_L) by 74.6% and the removal of total salt mass (R_M) by 62.6% within the 4% of the total removal time. Meanwhile, the groundwater discharge (Q') rose rapidly after a sharp decline from 100% to 40% in the first stage. As the residual saltwater wedge was retreated, the mixing intensity and removal efficiency decreased substantially in the second stage. Similarly, Q' raised with a declining rate at this stage. The removal efficiency was positively correlated with wall depth and hydraulic gradient and there were optimal distance of the middle spacing and height of lower dam to reach the highest efficiency. The groundwater discharge reduced monotonously with the increase of dam height and wall depth as well as the decrease of barrier spacing and hydraulic gradient. Under certain conditions, the efficiency of MPB in removing residual saltwater could be 40%–100% and 0%–56% higher than that of traditional subsurface dam and cutoff wall, respectively. The laboratory scale conclusions provide valuable physical insight for the real field applications regarding dynamic mechanism and regularity. These findings will always help decision makers choose proper engineering measures and protect groundwater resources in coastal areas.