Mesolithic Period (c.9000-5000 BC)
| Site | Type | County | Date (BC) |
| Pulli | settlement | Pärnu (W) | 9000-8550 |
| Siimusaare | settlement | Viljandi (SW) | 9000-5200 |
| Lammasmägi | settlement | Lääne-Viru (N) | 8700-4950 |
| Lepakose | settlement | Viljandi (SW) | 8000-6000 |
| Umbusi | settlement | Viljandi (SW) | 8000-5000 |
| Jälevere | settlement | Viljandi (SW) | 7200-6100 |
| Sindi-Lodja-I | settlement | Pärnu (W) | 7100-6700 |
| Sindi-Lodja II | settlement | Pärnu (W) | 6900 |
| Koru | settlement | Hiiu (I), (NW) | 5600-5100 |
| Kõpu peninsula | Complex | Hiiu (I), (NW) | 5500-5300 |
| Veibri | Cemetery | Tartu (SE) | 5200 |
The earliest traces of human habitation in Estonia were found at the Pulli settlement by the Pärnu River in the southwest and date back to approximately 9000 BC. These finds are associated with the Kunda culture (c.8500-5000 BC), a Mesolithic hunter-gatherer society that inhabited the Baltic forest zone spanning Estonia, Latvia, and into northern Russia. Named after the Lammasmägi settlement (c.8700-4950 BC) in Kunda, northern Estonia, the Kunda culture is believed to have evolved from the earlier Swiderian culture centred in modern-day Poland.
During the Mesolithic, the Baltic Sea basin was shaped by two opposing geological forces: glacio-isostatic uplift and eustatic sea-level rise. The Yoldia Sea stage (c.9700-8700 BC) began when the Baltic Ice Lake drained into the ocean through central Sweden, allowing saltwater to enter and create a brackish environment. Subsequently, the Ancylus Lake stage (c.8700-7500 BC) formed when rapid land uplift, resulting from the removal of the ice sheet’s weight, closed the shallow sills (submerged ridges or barriers that separate two deep water basins). This turned the basin back into a freshwater lake. A later regression in water levels shifted the shoreline near the present-day mouth of the Reiu River. During this late Ancylus/pre-Littorina transition, settlements were established, including the Sindi-Lodja-I site (c.7100-6700 BC) and the Sindi-Lodja II site (c.6900 BC), located approximately 400 metres further upstream.
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