This article treats a wide-ranging scientific project ‘The Evolution of the Baltic Sea and the Stages of the Earliest Human Settlement in the Southeast Baltic’ that started in 2009. The main research methods consist of multidisciplinary investigations of key archaeological sites and former glacial water-pools and bogs. The final result of the project is expected to be a model of demographic processes that occurred in the southeast Baltic during the Late Glacial and Early Holocene set against environmental changes.