Late Pleistocene to Holocene climate change of the Atlantic and the northern European realm is reflected by the facies of sediments in the Baltic Sea. The sedimentary sequence have been subdivided into zones reflecting the main postglacial stages of the Baltic Sea basin development according to sediment echosounder profiling and investigating sediment cores from the central Baltic. The changes in the environment of Baltic Sea bottom water is displayed by sediment physical, geochemical, and microfossil proxies. These proxies mark the main shift in the sedimentary facies of the Baltic Basin at 8.14 cal. years BP, from a freshwater to a brackish/marine environment due to the Littorina transgression of marine water masses from the North Sea. The downhole physical facies variation from the Eastern Gotland can be correlated basinwide. Thickness maps of the freshwater and the brackish sediments ascribe the general change in the hydrographic circulation from a coast-to-basin to a basin-to-basin system along with the Littorina transgression. Variations in the salinity of the brackish Littorina Baltic Basin are attributed to changes in the North Atlantic Oscillation (NAO) ascribing the wind forces driving the inflow of marine water into the Baltic Basin. Time series analysis of facies variation reveals distinct periodicities of 900 and 1,500 years. These periods can be compared with data from North Atlantic marine sediments and Greenland ice cores identifying global climate change effects in Baltic Basin sediments.