Cutoff walls have been widely used to control seawater intrusion (SWI) in coastal regions. However, previous research mainly focused on the protective effect of cutoff wall on the upstream groundwater system, the downstream groundwater deterioration of coastal aquifers (between the cutoff wall and sea) induced by the installation of cutoff walls was not clarified yet. We implemented indoor experiments and numerical simulations to investigate the downstream saltwater behaviors considering the construction of cutoff walls. The results revealed that cutoff walls could enable the rise of downstream saltwater wedge, widen the mixing zone width, mitigate the freshwater discharge, and aggravate the seaside groundwater deterioration in coastal aquifers. We further found that the wall opening size, wall distance to the sea, hydraulic gradient, and dispersivity could alter both the downstream spatial salt distribution and freshwater discharge, while hydraulic conductivity only affected freshwater discharge. It needs to be noticed that seawater invades the inland aquifer dramatically when the hydraulic gradient is less than 0.004 in our cases. Therefore, cutoff walls are not suitable for coastal aquifers with low hydraulic gradient. With the decrease of the distance between the wall and the sea boundary, the cutoff wall remains effective for the SWI control. Thus, we found that a cutoff wall closer to the sea can somehow minimize the groundwater salinization of coastal aquifers without increasing the construction cost. These results reveal the adverse side effects of the cutoff wall in downstream aquifer and further suggest additional countermeasures.