In order to understand the chemical characteristics of shallow groundwater, using the coastal areas in Qidong City, Jiangsu Province on the north of the Yangtze River Estuary, the Pudong New Area, Shanghai on the south of the Yangtze River Estuary, and the eastern Chongming Island as the study areas, the spatio-temporal distribution characteristics and formation mechanisms of chemical composition of shallow groundwater were investigated with mathematical and statistical methods and hydrogeochemical analysis methods. The results show that the shallow groundwater in the coastal area of the Yangtze River Estuary was hard water-hardest water and hard water during the wet and dry seasons, respectively, and was mainly fresh water. The main cations were Na+ and Ca2+, and HCO-3 was the anion with the highest content. The contents of main chemical components in the wet season were higher than those in the dry season, and the coefficient of spatial variation of each component in the wet season was larger than that in the dry season. Compared with Pudong, the chemical types of shallow groundwater in Qidong and the eastern Chongming Island showed a more significant seasonal change. The recharge of shallow groundwater mainly originated from atmospheric precipitation. The shallow groundwater in the coastal areas on the north of the Yangtze River Estuary and in the eastern Chongming Island were mainly affected by soil leaching, weathering and hydrolysis of rocks, cation exchange processes, and human activities, as well as evaporation and concentration to a certain extent, with only a few sites affected by seawater mixing. The coastal area on the south of the Yangtze River Estuary was mainly affected by weathering and hydrolysis of rocks and cation exchange processes and not affected by seawater mixing, and the agricultural activities had little influence on the area.