A partially preserved submerged prehistoric landscape, with several sites and a vast amount of stray finds from the early Mesolithic has been investigated by the Viking Ship Museum, prior to a development project in the Harbour of Køge, Denmark. Test pits excavated by mechanical excavator made it possible to document and sample the thick stratigraphy of the area. A reconstruction of the sedimentation of the prehistoric landscape was created by modelling and radiocarbon dating the local stratigraphy. The model shows the development of the area from an inland freshwater river system to a coastal lagoon, to transgression of the area by the sea, providing a landscape context to the archaeological sites in the area. After the pre-investigations with mechanical excavator, two sites were further excavated with divers. These sites consist of a partially dispositioned settlement material from the phase 1 of the Maglemose Culture (8000-7500 BC), as well as a fish weir, dated to the transition between the Maglemose- and the Kongemose Culture (c. 6800 BC).