We examine three questions concerning the post-glacial geological history of the eastern Gulf of Finland: (1) the amplitude of the Holocene sea-level regressions; (2) the time and mechanism of the development of large sand accretion forms (bars and spits), including dunes; and (3) the sea-level changes and coastal development over the last 4 kyr. Recent on-land geoarchaeological studies, as well as detailed marine geological research of the Gulf of Finland nearshore bottom, have provided new data for developing a hypothesis about the palaeogeographical development of the area. Geoarchaeological studies carried out around Sestroretsky Artificial Lake and within Okhta Cape, as well as analyses of previous studies of the Neolithic–Early Metal settlements, have shed new light on some aspects of coastal system development. Geographical information system (GIS)-based modelling of Holocene shorelines for the different time periods can be useful for future archaeological research. A series of submarine terraces was found at the bottom of the Gulf (sea depths from 10 to 2 m). The analysis of marine geological data (submarine terraces) and distribution of archaeological sites can be explained by a possible rise in relative sea level in the Gulf of Finland at 5 ka BP and a regression around 3 ka BP.