As a part of the East European Plain, Estonia is a flat territory, where uplands and plateau-like areas alternate with lowlands, depressions and valleys. These land forms, alongside with the coastal cliffs in northern and western Estonia, are the larger features of Estonian topography.

The bases of the uplands of Estonia are usually 75–100 m above sea level (a.s.l.). The highest point in Estonia and the Baltic States, Suur Munamägi Hill, is located in the middle part of the Haanja Upland. Erosional and accumulative uplands can be distinguished:

  • Erosional uplands are mostly flat. Their appearance depends largely on the bedrock topography. These uplands have a relatively thin Quaternary cover and the relief is dominated by moraine plains. The two erosional uplands in Estonia are The Pandivere Upland (the highest point: Emumägi Hill, 166 m a.s.l.) and The Sakala Upland (the highest point: Rutu Hill, 146 m a.s.l.).
  • The accumulative uplands have hilly topography. Their appearance is not dependent on the bedrock topography. Their relief is dominated by hills and valleys, built up of Quaternary sediments. The three accumulative uplands in Estonia are The Haanja Upland (the highest point: Suur Munamägi Hill, 317 m a.s.l.), The Otepää Upland (the highest point: Kuutse Hill, 217 m a.s.l.) and The Karula Upland (the highest point: Rebasejärve Tornimägi Hill, 137 m a.s.l.).
Other elevations include the Saadjärve Drumlin Field reaching 144 m
a.s.l., the West-Saaremaa elevation (54 m a.s.l.) and the Ahtme or Jõhvi
elevation (81 m a.s.l.).

Higher areas include also the plateaus. The Harju and Viru plateaus are located in northern Estonia and bordered on the north by the steep escarpment of the Baltic Klint. Both plateaus are about 30–70 m above sea level. The flat surface of the plateaus is occasionally cut through by river valleys and karst features. The erosion of the Harju Plateau has left some separate flat plateau-like hills: Toompea Hill and Viimsi Lubjamägi Hill in Tallinn and the Pakri islands. The relief of the Viru Plateau is formed by artificial features — oil shale pits and waste rock and ash hills.

The Ugandi Plateau (40–100 m a.s.l.) in southern Estonia is a sandstone plateau, cut by ancient valleys and bordered by high escarpments: the Tamme outcrop near Lake Võrtsjärv in the west and, the Kallaste outcrop on the beach of Lake Peipsi. Other relatively high areas are the Central-Estonian Plain (60–80 m a.s.l.) and Kõrvemaa (50–90 m a.s.l.).

The Lowlands are the plains reaching less than 50 m above sea level that have been flooded by the Baltic Sea, ancient Lake Peipsi and ancient Lake Võrtsjärv. The lowlands cover nearly half of the Estonian territory. The largest lowlands are located in western Estonia.

The West Estonian Lowland is a swampy plateau, with up to 20 m high limestone hills (Kirbla Hill, Mihkli Salumägi Hill, Salevere Salumägi Hill, etc.). The Pärnu Lowland is also swampy. Its bedrock is composed of Devonian sandstones. Its western margin at the sea coast is bordered by the highest dunes in Estonia.

The West Estonian Lowland extends to the West Estonian Archipelago. The relief is mostly flat and reaches 20 m a.s.l., except for the higher areas, including the West-Saaremaa elevation and its southern extension in the Sõrve Peninsula. The northern coast of Muhu and Saaremaa Islands is steep, up to 21 m at the Panga Cliff.

The North-Estonian Coastal Plain includes a narrow belt of land between the Gulf of Finland and the Baltic Klint. Its width is from a few metres to 20 km. The area includes several peninsulas and bays, and the islands of the Gulf of Finland. Low and swampy lowlands also occur west and north of the Lake Peipsi depression and in the Lake Võrtsjärv depression. The Alutaguse Lowland is situated north of Lake Peipsi.

Depressions and valleys are large features of relief, easily distinguished in South Estonia, where they separate the uplands. The Valga depression, 40–80 m a.s.l., is located between the Sakala and Karula Uplands and the Otepää Heights. The Väike-Emajõgi Valley, reaching Lake Võrtsjärv, is its northen extension. The Hargla depression, 70–100 m a.s.l., is located between the Haanja Heights and the Karula Upland. The Võru Valley is its extension, separating the Haanja and Otepää heights.

The Baltic Klint, also known as the North Estonian Klint in Estonia, is a remarkable feature of topography. It is one of the longest erosional escarpments in northern Europe, extending from Öland Island in Sweden to Lake Ladoga in Russia. In North-West and North-East Estonia, the Klint is often exposed as a coastal cliff of the Gulf of Finland. At Ontika, the highest point of the North Estonian Klint reaches 56 m a.s.l.

In most of the Estonian territory, the Palaeozoic sedimentary rocks are covered by Quaternary sediments. Most of the Palaeozoic bedrock outcrops occur in coastal cliffs near the sea and the larger lakes and in river valleys. All these outcrops have been formed by the erosive power of lakes, seas or rivers during the Pleistocene glaciation.

The present-day topography is largely a reflection of the bedrock geology. The deepening of the sea floor of the Gulf of Finland from Finland towards Estonia corresponds to the deepening of the crystalline basement. The rise of the sea floor towards the North Estonian limestone plateau corresponds to the erosional boundary of the Palaeozoic rocks under the sea. Another valley, in Central Estonia, oriented in the East-West direction, corresponds to the contact of hard Silurian limestones and soft Devonian sandstones.

The Estonian topography includes land forms that are more than 300 million years old, re-opened during more recent erosion. The final retreat of the seas that formed the Palaeozoic sedimentary rocks of Estonia took place at the end of the Devonian era (about 350 million years ago). It left a flat sandy plateau, extending from Finland to Latvia, from Russia to Sweden, and even further. The erosion processes, responsible for cutting the depressions in the Gulf of Finland and Central Estonia, started in the beginning of the Cenozoic (about 65 million years ago) and lasted until the Pleistocene glaciation (about 2 million years ago). Then, the North Estonian Klint was as high as 150 m, separating the northern margin of the limestone plateau from the ancient river, running in the present depression of the Gulf of Finland. The pre-Devonian features of topography — Pandivere Upland, the Ahtme elevation and the Narva River Plateau were re-exposed.

The Pleistocene glaciers formed the topography of Estonia, by levelling off some features and by accumulating new land forms.

About 12 000 years ago, most of Estonia was covered by the Baltic Ice Lake. About 7000 years ago, the predecessor of the Baltic Sea, the Litorina Sea, covered the coastal areas of the present northern and western Estonia. As the ice margin retreated, the uplands of Estonia, including the Pandivere Upland and the Haanja, Otepää and Sakala heights became free from ice as terrestrial areas. The lowlands, however, were abraded. The deposition of thin sequences of varved clays and sands in lowlands made the surface topography even flatter.

The topography after the Ice Age is very different from that before the Ice Age. Besides the erosion and accumulation activities of the ice, there are two important aspects:

  • Since before the Ice Age, the sea level has risen more than 100 m, covering former land areas and forming the Baltic Sea and its bays. The escarpments (the klints) have lost two thirds of their height.
  • Heavy glaciers pushed the surface several hundreds of metres deeper, as compared to the position before the Ice Ages. After the ice retreated, a compensatory land rise began. It continues today in NW Estonia, reaching 2–3 mm per year. This has resulted in a slow, but steady growth of the land area. New islets have formed in the Väinameri area and elsewhere near Hiiumaa and Saaremaa Islands.

Mires have also contributed to the flattening of the surface topography. The oldest mire deposits in Estonia are about 8000 years old. The most intense peat formation in bogs has taken place during the past 2000 years. The mire lowlands cover more than 1/5 of the Estonian territory.

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