The paper provides original data that shed light on the formation dynamics of Lake Chaika, which is situated in the central part of the Curonian Spit and is the only large water body in the sand spits of the southeastern Baltic. Based on the multi-proxy approach, incl. investigation of the lithological structure of the bottom sediment cores, loss-on-ignition analysis, diatom analysis, study of macrofossil remains, and radiocarbon dating, we revealed that Lake Chaika was formed already in historical time, around 200 years ago. Before this period, the lake kettle, presumably, has not submerged during the Littorina transgressions, enabling the terrestrial development of the ecosystems on the moraine protrusion. During the mid-late Holocene (6700–150 cal BP), this depression was occupied by the peat-forming fen and alder carr communities. The peat deposits are separated from the overlying layers of gyttja by the thin sand horizon. We consider it a time marker for the so-called “sand disaster”, which occurred on the territory of the Curonian Spit in the 18th century (≈1700–1800). The change in the hydrological regime of the lake launched the ecosystem shifts during the last two centuries: from the water body to a wetland and vice versa. It is stated eight formation phases of the lake’s ecosystem: the terrestrial development without wet habitats (8900–6700 cal BP), the period of alder carrs (6700–3400 calBP), the sedge fen period (3400–450 cal BP), the period of inundated forest (1500–1700 AD), the “sand disaster” period (1700–1800 AD), the period of eutrophic water body (1800–1900 AD), the period of terrestrialised wetland (1900–1950 AD), and the period of secondary development of eutrophic water body (after 1950 AD).