The seafloor of the eastern Gulf of Finland (the Baltic Sea), especially its easternmost part – Neva Bay – has experienced anthropogenic impacts since the beginning of the XVIII century. The aim of this paper is: i) to analyze results of different stages of anthropogenic impact on the geological environment and ecosystem, ii) to assess the influence of dredging, dumping, and aggregates (sand, gravel) and ferromanganese concretions extraction on bottom relief and sedimentation processes, and iii) to establish the major spatial and temporal trends of heavy metal accumulation in the soft bottom sediments. Since the establishment of St. Petersburg, and into the 1960s, there was a physical impact on the seabed through the construction of artificial islands, dredging, and dumping. From 1960s to the 1990s, these types of activity became even more intense, as nearshore submarine terraces were used for sand and gravel extraction, and sediment pollution (e.g., heavy metals) has become one of the main environmental problems of the region. Based on extensive geochemical data collected for the first time in the study area, we examined a vertical distribution of heavy metals in cores obtained from different sedimentary basins. Results demonstrate a trend of increasing concentration values from the 1940s to the 1990s. Background concentrations of heavy metals are based on the geochemistry of catchment areas, decreasing in concentrations from the northwest to the southeast, while the maximum concentrations of hazardous substances deposited from the 1970s to the 1990s were observed in the easternmost part of the gulf. Since the 1990s the heavy metal input to the Gulf of Finland has significantly decreased, so the concentration of these hazardous substances in the surface sediments dropped as well, demonstrating a spatial distribution corresponding more to background (natural, pre-industrial) values. On the other hand, big hydrotechnical projects, realized during the last 20 years – artificial territories and new harbors construction, accompanying with dredging and dumping, ferromanganese concretion extraction, etc. – led to resuspension and secondary pollution of water. The other problem is the expansion of anoxic areas, caused both by climate change and human-stimulated eutrophication. Near-bottom anoxic conditions stimulate heavy metal migration from bottom sediments into the water column. All these processes impacted benthic communities as our review of previously published studies reveals. Geological and geophysical research revealed that within some areas anthropogenic impact caused a complete change of the sedimentation processes such as direction and rates of transport, which led to the total transformation of bottom relief, surface sediment distribution, and the benthic communities.