During late- and post-glacial times the Baltic basin has been periodically isolated from the Atlantic and freshwater and saline conditions have alternated. This is a consequence of the interactions between the spatially variable glacial rebound of the region and the simultaneous eustatic sea-level rise in the adjacent Atlantic. Observations of the timing of these isolations and of the location of the barriers therefore provide constraints on the rebound models. High resolution numerical models of rebound of southern Sweden, the Danish straits, and the Baltic have been developed and tested against observations of lake-level change as well as against the observed elevations of the Last Baltic Ice Lake shoreline which formed before about 10.3 ka bp. Predictions of sea- and lake-levels are used to test two alternative hypotheses about the ice thickness over Scandinavia and to estimate parameters that describe the Earth’s response. Optimum values for the latter are: lithospheric thickness of 60 ± 20 km, upper-mantle viscosity of 3.3 × 1020 Pa s, and lower-mantle viscosity of 1022 Pa s. The rapid lake-level fall at the end of the Baltic Ice Lake stage is estimated to be 30 ± 5 m. The optimum ice model for Scandinavia is one in which the ice thickness over southeastern and southern Scandinavia was relatively thin compared with the ice thickness over Sweden and Norway: the ice thickness in the southeast and south changes slowly with distance inwards of the ice margin whereas over Sweden and Norway the ice thickness profiles are considerably steeper. The earth and ice models have been combined with high-resolution digital terrain data to develop a comprehensive model for the evolution of the Baltic basin since the time the area last became ice free. The reconstructions predict the occurrence of barriers at certain times which impede free flow between the Atlantic and Baltic and confirm that the Baltic lake levels are controlled by rebound at four localities; Degerfors in the Närke region of southern-central Sweden, the Vänern outlet through the Göta Älv, Öresund, and the Darss–Langelands–Store bælts in Denmark.