The marine-freshwater environmental transition, i.e. basin isolation from the Limnea Sea, has been identified in two short sediment cores with respect to their diatom composition, loss-on-ignition and magnetic susceptibility content. The isolation level of the basins was dated by accelerator mass spectrometry radiocarbon measurements. The basins are situated on the southern coast of the Gulf of Finland between altitudes 5.5 and 3.9 m above sea level. The Lohja basin became isolated from the sea around 2300 cal yr BP and K smu basin around 1800 cal yr BP as a result of glacio-isostatic uplift. The total land upheaval rate that has been 2.6 mm yr –1 since 2500 cal yr BP has currently decreased to 2.0 mm yr –1. We present a GIS-based 3D palaeogeographic reconstruction of the palaeocoastline changes in northern Estonia for two peninsulas, P rispea and K smu, as well as compose a shoreline displacement curve for the study area, which is a compilation of previous and ongoing investigations.