Sediment records in the Baltic Sea image the development of late Glacial and Holocene climate in Northwestern Europe, the transgression of global sea level and the flooding of the shelf, and the effects of isostatic uplift of Scandinavia. Changes in salinity of surface and deep waters were pronounced to approximately 5,000 years before present and were mainly caused by sea level rise and sill subsidence. Density stratification between salty deep and fresher surface waters caused the development of anoxic conditions and deposition of laminated sediments on large parts of the sea floor in the Baltic proper. Blooms of cyanobacteria were more intense than today, and the Baltic Sea was a fertile environment that supported diverse and abundant coastal resources nourishing Mesolithic Man. At 5,000 years before Present, the climate deteriorated at the transition from the Atlantic to the Sub-Boreal climatic period. Early Neolithic agricultural communities spread from the South to the North and replaced foragers, initiating the clearing of forests in the Baltic Sea catchment. The salinity of the Baltic Sea decreased, oxygenation of deep seafloors was improved, and fertility of the sea surface was significantly reduced, as seen by low accumulation rates of organic carbon in bioturbated sediments. From approximately AD 1,000 on, salinity rises again and anoxic periods are more common. A clear impact of human activity in the catchment is seen in sediment records of the last 100 years, with increased burial rates of nutrient elements from fertilisers and trace elements. On the other hand, climate continues to govern changes in the salt budget and influences the balance between oxic and anoxic conditions at the seafloor that have a large impact on nutrient budgets in the water column.