The crust is part of the East European Craton and formed beginning in the Paleoproterozoic nearly two billion years ago.
Shallow marine environments predominated in Estonia, producing extensive natural resources from organic matter such as oil shale and phosphorite.
The Mesozoic and much of the Cenozoic are not well-preserved in the rock record, although the glaciations during the Pleistocene buried deep valleys in sediment, rechanneled streams and left a landscape of extensive lakes and peat bogs.
The Old Red sandstones deposited in the Middle Devonian in a nearshore marine environment from sand and silt, shed during the Caledonian orogeny onto the Fennoscandian continental plain.
The sedimentary rocks preserve extensive fossils and tens of thousands of specimens have been gathered at the University of Tartu and Institute of Geology.
Through the Devonian, the continent Baltica, which included Estonia, drifted from the South Pole to north of the Equator and was influenced by glacier-related changes in sea level.
The Kärdla astrobleme on Hiiumaa Island formed from an asteroid impact 455 million years ago, and Estonia has three other small meteorite craters, less than 110 meters in diameters in the bedrock.
The Baltic Sea and Gulf of Finland are relatively deep erosional features in the bedrock, as are the lake basins of Vortsjarv and Peipsi, which were deepened by glaciers during the Pleistocene.
Before and in-between glaciations, a network of deep valleys formed, up to 145 meters below sea levels, connecting the Baltic and the Gulf of Finland.
Glacial debris is less than five meters thick in northern Estonia and parts of the country underlain by limestone and dolomite have karst processes and hardly any remnants of glaciation.
The Kaali meteorite crater on Saaremaa Island was the first geologic site slated for protection after its recognition in 1937.
Since the 1950s, Estonian organizations drilled tens of thousands of boreholes through the sedimentary cover, in some cases reaching more than 500 meters deep into the crystalline basement rock.