Seawater intrusion poses a major threat to freshwater resources in coastal aquifers worldwide. In China alone, these types of aquifers provide a vital groundwater source for nearly 400 million people. Whereas modern seawater intrusion is often attributed to human activities and climate change, the role of paleo–salt water remains poorly quantified. This continental-scale investigation of seawater intrusion in China reveals that paleo–salt water, not modern seawater, dominates salinity patterns in large sedimentary basins. Analysis of over 2100 water samples shows a strong correlation between intrusion and tectonic subsidence zones, with paleo–salt water affecting 66% of the observed salinized areas. In northern coastal plains, paleo–salt water trapped in confined aquifers is characterized by salinity levels exceeding 144.6 grams per liter, whereas modern seawater intrusion (34%) occurs in hilly regions with thinner sediments. Isotopic signatures (δ¹⁸O) trace paleo–salt water intrusion to Quaternary sea level changes. These findings improve seawater intrusion source identification and inform global salinity management.