The Middle-Late Holocene infill of the coastal plain of Marathon, Greece, consists of lagoonal deposits related to the decrease of the sea level rise rate. Between a little earlier than 5800 and 3500 Cal BP, mesohaline-oligohaline lagoonal carbonate muds were uninterruptedly accumulating in the central and more seaward areas of the embayment. At the same time in the nearshore environment, oligohaline pelloidal charophytic muds were deposited during periods of a relatively increased rate of sea level rise, whereas during periods with lower rates of sea level rise, extensive marshes were forming in supratidal settings. The formation of framboidal pyrite and evaporitic minerals point to a periodic anoxic, sulfidic, and schizohaline environment. In addition, a warm, strongly seasonal climate under the influence of resurgent continental groundwater is suggested. After 3500 Cal BP, the lagoon witnessed a relatively abrupt change to palustrine mud deposition. The embayment was frequently exposed, and communication with the sea was not perennial. This period, terminated at about 2400 Cal BP, is most likely associated with a wetter and probably more temperate climate. The uppermost depositional unit is dominated mostly by fluvial sediments deposited in a wetland with no recorded communication with the sea. The sea level rise, indicated by several peat formations, is estimated to be lower than that predicted by the glacio-hydroisostatic model and the data from other Greek areas that are considered relatively stable. Hence, a tectonic uplift of the area is suggested at a rate of about 0.4–0.5 mm/y, which almost counterbalances the predicted rate of relative sea level rise of about 0.6–0.7 mm/y for the last 2000 years. This is a plausible explanation for the relative geomorphological stability, since at least Classical times, suggested by the historical documents.