Chemical analysis of groundwater in petroliferous basins can be an effective way to determine the regional hydrogeological regime and to evaluate the preservation conditions of hydrocarbons. This paper presents the hydrochemical distribution of both individual aquifers and different structural units within the Palaeogene strata of the Gaoyou subbasin in the North Jiangsu Basin, east China. The results show that the salinity of the Palaeogene aquifers in the Gaoyou subbasin displays a systematic increase from the central deep depression to the periphery areas, and shows a reverse trend as the burial depth increases. Salinity maps of individual aquifers suggest that formation water in the deep layers at the centre of the study area probably retains original features of fresh lake water. Geofluids near the central deep depression of the Gaoyou subbasin migrate vertically through the Zhenwu and Hanliu faults, while those of the northern slope belt mainly flow laterally through aquifers. Both low and high salinity formation water can be found in the hydrocarbon producing areas. The low salinity zones commonly affected by infiltrated meteoric water are unfavourable conditions for the preservation of trapped hydrocarbons.