Surface water is all inland water, either standing or running (except for groundwater, transitional waters and coastal waters). Bodies of surface water are divided into watercourses (rivers, brooks and ditches) and stagnant water (lakes, ponds).
The status of surface water depends on the efficiency of wastewater treatment, the intensity of agriculture and protection measures used in agriculture. Since 1992, the pollution load of surface water has decreased significantly in Estonia, due to building new water treatment plants, renovating old ones, and decrease in agricultural production.
The status of surface water is monitored by bodies of surface water; there are currently 750 bodies of surface water whose status has to be determined. Environmental register includes more water bodies than bodies of surface water. Usually, one larger water body in the environmental register (bodies of stagnant water with the water mirror area starting from 50 ha, flowing bodies of water with the catchment area starting from 10 km²) forms a body of surface water. Some big water bodies are divided into several bodies of surface water, while some smaller watercourses are drawn together into one larger watercourse. One body of surface water has a similar natural type, living environment, and human impact.
In the end of 2008, the report „Ecological Status of Estonian Bodies of Surface Water in 2004-2008” was compiled for the first time. On the basis of this report, the status of 750 bodies of surface water was determined.
Due to chemical status, the overall status is bad only in four watercourses. In other bodies of surface water of a poor, bad or very bad status, the ecological status is problematic. For these bodies of surface water, the status of which is poor, bad or very bad, a plan of measures for improving the status shall be compiled. The measures for improving the status of bodies of surface water exist in a written format in river basin management plans on river basin districts.
Lakes with artificial water bodies comprise approximately 5% of the territory of Estonia, that is, we have the average of 1 lake by each 40–50 km² of the territory. Lake Peipus and Võrtsjärv belong among the largest lakes in Europe.
Estonia has approximately 1200 tarns and reservoirs, the area of which is larger than 1 ha. The location of lakes is extremely uneven. There are more lakes in South-East and South Estonia with the approximate of 30 lakes by 100 km² (in Harju County, the vicinity of Jussi-Järvi-Koitjärve, and in Valga County, in Karula and Otepää). In contrast, in West and Central Estonia, there are extensive areas totally without lakes.
There are no very deep lakes in Estonia. The lake of the greatest depth is Rõuge Suurjärv – 38 m. The depth of Lake Peipus reaches 18 and the depth of Võrtsjärv to 6 metres.
Seven limnological fields may be distinguished in Estonia: oligotrophic and dystrophic lakes in South-East Estonia, oligotrophic and dystrophic lakes of North-East Estonia, eutrophic lakes of uplands, Pandivere alkalitrophic lakes, dystophic lakes of the transition zone of Estonia, dyseotrophic lakes of Estonian lowland, and halotrophic lakes of West Estonia.
With reference to fishery and recreation economy, most valuable lakes are located on the Otepää and Sakala upland and Vooremaa. Other regions are richer in plant and animal rarities.
Nationally observed lakes are Lake Peipus, Võrtsjärv and small lakelets, Nohipalu Black Lake (Nohipalu Mustjärv), Nohipalu White Lake (Nohipalu Valgjärv), Pühajärv, Rõuge Big Lake, Lake Uljaste, Viitna Long Lake, Lake Ähijärv, and Mullutu Suurlaht (Big Bay). On Lake Peipus and Võrtsjärv, observations on hydrochemistry are conducted by Tartu Environmental Research and in terms of biology by Võrtsjärve Limnological Station of the Zoology and Botany Institute of EULS. Both the hydrochemical and biological monitoring of lakelets is conducted by the Võrtsjärve Limnological Station.
In the 1970s and 1980s, Estonian lakes were heavily influenced by fertilizers and sewage, which caused quick eutrophication. With the crumbling of collective farms, agricultural production lie dormant; the status of lakes, especially lakelets, started to improve in the beginning of the 1990s. Eutrophication slowed, as the content of nitrogen decreased in lake water. With the improvement of the economic situation, the new rise in eutrophication may be expected in the near future.
Estonian rivers are short, with a small catchment area, and therefore also relatively scare in water. The river system, however, is dense. Runoff forms mostly on the state territory. Fragmentation of water sources into small water bodies and their uneven distribution limits possibilities for using them.
Drainage divides separate Estonian rivers into four natural river basin districts: Narva-Peipsi river basin district, the Gulf of Finland river basin district, the Gulf of Riga river basin district, and the river basin district of islands. The rivers of three river basin districts – Narva-Peipsi, the Gulf of Finland and the Gulf of Riga river basin district – start from the slopes of the extensive karst area of Pandivere upland.
There are 10 rivers longer than 100 km. Longest is the Võhandu River – 162 km, then the Pärnu River – 144 km. These are followed by the Põltsamaa, Pedja, Kasari, Keila and Jägala River.
There are 15 rivers with catchment areas larger than 1000 square kilometres, whereas the entire catchment area of the Narva River is larger than the territory of the Republic of Estonia. The catchment area of the River Emajõgi, located almost in its entirety in Estonia, forms 22% of the state territory.
The river with the largest fall is Piusa; the altitude distance of its source and mouth is 208 m. The largest fall, 3.5 m/km is on the River Mustoja, which flows into the Gulf of Finland, while the lowest on Emajõgi with 0.04 m/km, where the fall per 100 km is only 3.7 m.
The specificity of Estonian nature lies in the occurrence of the karstic feature (subsurface streams, swallow holes, etc) in North Estonia and islands. Due to karst, some rivers flow partly underground (Jõelähtme, Tuhala, Kuivajõgi and others). Pandivere region is characterised by the difference in the borders of ground and underground catchment areas.
Hydrology monitoring network on Estonian rivers and lakes was formed in the 1920s and therefore we can use long-term observation data. Currently, 40 observation stations are being used.
There are few rivers rich in water in Estonia. In terms of water abundance, the Narva River holds the first place. As for the runoff of Estonian rivers, 23% flow into the Gulf of Finland, 43.6% into the Gulf of Rigs, 33% into Lake Peipus and the Narva River, and 0.3% into Russia and Latvia.
The distribution of annual successive runoff of Estonian rivers varies. Spring floods usually form from the snowmelt water and occur on most of the rivers at the same time from March to April, except for the Narva River and the River Emajõgi, with a strongly regulated runoff. Summer minimum usually begins in the middle of June and ends in the middle of September or the beginning of October (apart from the Narva River and Emajõgi). The climax of autumn runoff occurs in November. The low-flow period in winter lasts from January to March. The extent of minimum runoff in winter and summer is almost equal.