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A seawater intrusion experiment was carried out in a shallow coastal unconfined aquifer at Skansehage, Denmark. The aquifer consists of 6–10 m of postglacial (Holocene) eolian and marine sands and gravels resting on Pleistocene glacial sequence of tills and glacio- fluviatile sediments on a basement of Palaeocene (Danian) limestone. Stable isotopes (18O and 2H), strontium isotopes (87Sr/86Sr) and the elements Sr and Cl were measured to delineate the mixing of seawater and groundwater in the shallow aquifer and to determine the contribution from different water sources along the flow paths. The stable isotopes reflect recharge conditions and mixing between groundwater and seawater. The 87Sr/86Sr isotope ratios are controlled by aquifer matrix chemistry. The 87Sr/86Sr ratio distribution and Sr content reveal a ternary mixing system in the shallow aquifer, encompassing brackish seawater, fresh shallow groundwater and deep groundwater from the underlying limestone aquifer as end-members. A mixing analysis is performed using the Cl contents and the 87Sr/86Sr ratios. The mixing analysis indicates a zone with leakage of deep groundwater from the limestone aquifer into the lower part of the shallow sandy aquifer through the Pleistocene sedimentary sequence. The upper part of the sandy aquifer is thoroughly dominated by mixing processes between infiltrating fresh groundwater and brackish seawater from Isefjord. Prior to the intrusion experiment there appeared to be limited mixing between the upper and lower part of the water body in the shallow sandy aquifer. The leakage of deep groundwater increased during the intrusion experiment as a result of the large abstraction of groundwater. Following the ceasing of the groundwater pumping, the interface went from being vertical to being predominantly horizontal due to density flow. As a consequence the deep groundwater from the limestone aquifer was pushed by the seawater into the upper part of the aquifer to mix with the upper fresh groundwater.