Estonia's land border with Latvia runs 267 kilometers; the Russian border runs 290 kilometers. From 1920 to 1945, Estonia's border with Russia, set by the 1920 Tartu Peace Treaty, extended beyond the Narva River in the northeast and beyond the town of Pechory (Petseri) in the southeast. This territory, amounting to some 2,300 square kilometres (888 sq mi), was incorporated into Russia by Stalin at the end of World War II. For this reason the borders between Estonia and Russia are still not defined.

Estonia lies on the eastern shores of the Baltic Sea immediately across the Gulf of Finland from Finland on the level northwestern part of the rising East European platform between 57.3° and 59.5° N and 21.5° and 28.1° E. Average elevation reaches only 50 metres (164 ft) and the country's highest point is the Suur Munamägi in the southeast at 318 metres (1,043 ft). There is 3,794 kilometres (2,357 mi) of coastline marked by numerous bays, straits, and inlets. The number of islands and islets is estimated at some 1,500. Two of them are large enough to constitute separate counties: Saaremaa and Hiiumaa. A small, recent cluster of meteorite craters, the largest of which is called Kaali is found on Saaremaa, Estonia.

Estonia is situated in the northern part of the temperate climate zone and in the transition zone between maritime and continental climate. Estonia has four seasons of near-equal length. Average temperatures range from 16.3 °C (61.3 °F) on the Baltic islands to 18.1 °C (64.6 °F) inland in July, the warmest month, and from -3.5 °C (25.7 °F) on the Baltic islands to -7.6 °C (18.3 °F) inland in February, the coldest month. The average annual temperature in Estonia is 5.2 °C (41.4 °F). The average precipitation in 1961–1990 ranged from 535 to 727 mm (21.1 to 28.6 in) per year.

Snow cover, which is deepest in the south-eastern part of Estonia, usually lasts from mid-December to late March. Estonia has over 1,400 lakes. Most are very small, with the largest, Lake Peipus, (Peipsi in Estonian) being 3,555 km2 (1,373 sq mi). There are many rivers in the country. The longest of them are Võhandu (162 km or 101 mi), Pärnu (144 km or 89 mi), and Põltsamaa (135 km or 84 mi).[89] Estonia has numerous fens and bogs. Forests cover 61% of Estonia. The most common tree species are pine, spruce and birch.[93] Phytogeographically, Estonia is shared between the Central European and Eastern European provinces of the Circumboreal Region within the Boreal Kingdom. According to the WWF, the territory of Estonia belongs to the ecoregion of Sarmatic mixed forests.