Differential glacio-isostatic movement and climatically controlled eustatic change has caused transgression and regression in the Baltic Sea during its Holocene development. In the southern Baltic, glacio-isostatic subsidence superimposed with eustatic rise has provoked a continuously retreating coastline since the beginning of the Littorina transgression, 8000 BP. On the contrary, at the same time, uplift of the Fennoscandian Shield has caused permanent regression along the Scandinavian coast. An especially developed numerical space/time model displays the transgression and regression processes. Along the southern sinking coast, the entire ecosystem, including the conditions for human settlements, is influenced by the sea transgression. The complex processes require interdisciplinary research teams consisting of geoscientists (geologists, geomorphologists, geodesists), biologists (paleobotanists, paleozoologists), climate researchers, and archaeologists to study the complex processes affected by retreating coastlines and their socioeconomic implications. Such a team has investigated, since September 2002 along the southern Baltic Sea coast, the cause and effect relation between driving forces (climatic and geological processes) and the response of the natural and social environment in the coastal areas of a transgressive sea. Since 1999, underwater archaeological studies have discovered Mesolithic and Neolithic settlements along drowned coastlines of the Mecklenburgian Bight. Dated artifacts helped to describe the relative sea level change in the western Baltic Sea. On the basis of these data, methods of backstripping have been developed to describe, at a high resolution, the process of coastal development along a sinking coast of a tideless sea. Greenhouse gas emission scenarios provided by the Intergovernmental Panel on Climate Change and their effects on sea level change have been coupled with predictions of isostatic vertical crustal movement, resulting in scenarios of future coastline development. Those scenarios help to elaborate protection strategies in the frame of long-term planning in coastal zone management.