Abstract An explanation is presented for the origin of brackish to saline groundwater in the coastal area of the Netherlands based on geological, chemical (chlorinity), isotopic and geophysical data. A critical review of all possible salinization mechanisms shows that the origin of the brackish water is related to former transgressions. Both the vertical salinity distribution and the carbon-14 activity of the groundwater indicate that connate sea water from the Pliocene to Early Pleistocene is not the source of the brackish to saline waters in the overlying Pleistocene fluvial aquifers. Instead, it derives from Holocene transgressions. The salinization mechanism is discussed in relation to the paleogeographical development during the Holocene and the occurrence of low-permeability strata. Finally, freshening of the aquifers following retreat of the sea is briefly considered.