The surface water Subei Plain was polluted eriously, and the deep confined groundwater becomes the main exploitation aquifer, but high-water levels areas still exist after the extensive groundwater extraction. In order to investigate the cause of this phenomenon, the hydrogen and oxygen isotopes as well as water chemistry of river water and groundwater in Lianyungang,Huaian, Yangzhou, Taizhou and Yancheng were sampled and analyzed. The results showed that the hydrogen and oxygen isotopes of confined water in the Subei Plain are depleted relative to the surface water and the shallow groundwater, rather than from local infiltration of precipitation and recharge of the upper aquifer by transgressive flow. The recharge source is characterized by the obvious isotope depletion. Tritium dating data indicates that the groundwater receives modern precipitation recharge and apparent tritium from nuclear testing has been detected in the confined water. The large amount of metasilicic acid in the deep groundwater indicates that the groundwater water-rock reaction is dominated by the silicate reaction. Because multiple volcanic eruptions have occurred since the Pliocene in the northern Jiangsu area, the area of occult basalt beneath the Quaternary strata may be the main aquifer where deep groundwater reacted with water-rock to produce the metasilicic acid, and these metasilicic acid-rich groundwater then transported through the faults to the Quaternary confined aquifer.