With the exploitation of urban underground spaces, deep foundation pit constructions increasingly are evaluated. Pits in soft soil areas adjacent to operating subway are especially difficult to excavate. After indoor testing of water drainage for a station on the Shanghai Metro line 9, and on the basis of treatment and analysis of water level drain hole and flux monitoring data, pore water pressure, layered settlement and surface soil settlement, we summarize the relationship between factors influencing settlement during water drainage. This research offers design experience and blueprints for water drainage and ensures the safety of metro pit construction and enclosure structure stability.