The stress on the environment is increasing as the human population living on it increases. Water eutrophication, a leading cause of impairment of many freshwater and coastal marine ecosystems in the world, is a typical consequence of anthropogenic pressure on the environment. The Baltic Sea represents an excellent example of eutrophication-related massive bottom water deoxygenation since 1950s, when the nutrient inputs derived from agricultural fertilisers and wastewater discharges increased significantly. Faecal lipids (beta-stanols) represent a tool to estimate qualitatively anthropogenic sewage pollution in the environment. The present study shows that a ratio to evaluate sewage pollution based on faecal beta-stanols preserved in modern sediments reflects the eutrophication status of the Baltic Sea and rivers from its catchment area, as well as the nutrient inputs in the central Baltic Sea since 1860. A second ratio, which allows differentiating between livestock breed and human faecal matter, reflects human population growth in the Baltic Sea Eastern European countries since 1860, and more specifically in St. Petersburg. Sedimentary faecal biomarkers are thus reliable indicators for both population growth and anthropogenic sewage pollution in the Baltic Sea, and may thus be useful to evaluate the past and present status of this environment.