Maintenance of groundwater level is an important issue toward resolving land subsidence problems in delta regions; this process includes two major mechanisms: recharge and discharge. However, the overuse of groundwater in coastal aquaculture or agriculture, from the perspective of discharge, is still viewed as the major issue which causes the problem of land subsidence in many Asian countries. This article focused on the significant decrease in infiltration in history, from the perspective of recharge, to explore land subsidence. Through the three-by-three layer approach, we demonstrated that decisive intervention by man-made landscapes, including dike construction, river reclamation, and establishment of built areas, which can date back to the Japanese colonization about 100 years ago, has significantly changed waterways in Taiwan. This intervention induced a tremendous reduction in groundwater infiltration and subsequently has a close relationship with the serious land subsidence that is occurring in the southwestern coastal regions. The abuse of groundwater by fishermen for aquaculture in recent decades might just be the last factor in a series of events to cause a sinking land. This paper argues that a certain ratio of land should be restored for the purpose of groundwater recharge to amend the effect of the man-made intervention on the natural water system. In addition, in accordance with the sedimentation features of deltas, areas located at the top of the alluvial fan of a delta, which have porous soil structures, bear greater responsibility for infiltration.