Post-glacial aquatic ecosystems in Eurasia and North America, such as the Baltic Sea, evolved in the freshwater, brackish, and marine environments that fringed the melting glaciers. Warming of the climate initiated sea level and land rise and subsequent changes in aquatic ecosystems. Seminal ideas on ancient developing ecosystems were based on findings in Swedish large lakes of species that had arrived there from adjacent glacial freshwater or marine environments and established populations which have survived up to the present day. An ecosystem of the first freshwater stage, the Baltic Ice Lake initially consisted of ice-associated biota. Subsequent aquatic environments, the Yoldia Sea, the Ancylus Lake, the Litorina Sea, and the Mya Sea, are all named after mollusc trace fossils. These often convey information on the geologic period in question and indicate some physical and chemical characteristics of their environment. The ecosystems of various Baltic Sea stages are regulated primarily by temperature and freshwater runoff (which affects directly and indirectly both salinity and nutrient concentrations). Key ecological environmental factors, such as temperature, salinity, and nutrient levels, not only change seasonally but are also subject to long-term changes (due to astronomical factors) and shorter disturbances, for example, a warm period that essentially formed the Yoldia Sea, and more recently the “Little Ice Age” (which terminated the Viking settlement in Iceland). There is no direct way to study the post-Holocene Baltic Sea stages, but findings in geological samples of ecological keystone species (which may form a physical environment for other species to dwell in and/or largely determine the function of an ecosystem) can indicate ancient large-scale ecosystem features and changes. Such changes have included, for example, development of an initially turbid glacial meltwater to clearer water with increasing primary production (enhanced also by warmer temperatures), eventually leading to self-shading and other consequences of anthropogenic eutrophication (nutrient-rich conditions). Furthermore, the development in the last century from oligotrophic (nutrient-poor) to eutrophic conditions also included shifts between the grazing chain (which include large predators, e.g., piscivorous fish, mammals, and birds at the top of the food chain) and the microbial loop (filtering top predators such as jellyfish). Another large-scale change has been a succession from low (freshwater glacier lake) biodiversity to increased (brackish and marine) biodiversity. The present-day Baltic Sea ecosystem is a direct descendant of the more marine Litorina Sea, which marks the beginning of the transition from a primeval ecosystem to one regulated by humans. The recent Baltic Sea is characterized by high concentrations of pollutants and nutrients, a shift from perennial to annual macrophytes (and more rapid nutrient cycling), and an increasing rate of invasion by non-native species. Thus, an increasing pace of anthropogenic ecological change has been a prominent trend in the Baltic Sea ecosystem since the Ancylus Lake. Future development is in the first place dependent on regional factors, such as salinity, which is regulated by sea and land level changes and the climate, and runoff, which controls both salinity and the leaching of nutrients to the sea. However, uncertainties abound, for example the future development of the Gulf Stream and its associated westerly winds, which support the sub-boreal ecosystems, both terrestrial and aquatic, in the Baltic Sea area. Thus, extensive sophisticated, cross-disciplinary modeling is needed to foresee whether the Baltic Sea will develop toward a freshwater or marine ecosystem, set in a sub-boreal, boreal, or arctic climate.