Võrtsjarv is the largest lake within the boundaries of Estonia. Not considering Lake Peipsi on the Russian border, it surpasses all other Estonian lakes together by the surface area. The few islands are mostly located in the southern part of the lake. Tondisaar and Pähksaar are permanent islands while Ainsaar turns into a peninsula during low water, and Heinassaar is flooded in high water periods. The shores of Võrtsjarv are mostly low: swampy in the southern part, and sandy in the northern part; the eastern shore is higher. Despite its large surface area, the lake is shallow. The deepest place lies between the eastern shore and the island of Tondisaar along the submerged elongation of the riverbed of the Väike Emajõgi River. The lake depression is of preglacial origin but has somewhat been influenced by glaciers. On the eastern shore the Devonian sandstone bedrock is denuded along
a stretch of several kilometres. This abrasion shore at Tamme is 3 - 8 m high and subjected to protection as a fam
ous finding-place of fossil placoderm fishes. In the southern part the lake bottom is covered with a mud layer up to 5.5 m thick, which is gradually being replaced by sandy mud and sand in the direction of north; the mud is lying on the marl. The total thickness of sediments increases southwards, up to 7.6 m.
Võrtsjärv has tens of inflows collecting their water in three counties, on
a catchment area exceeding the lake surface twelve times. Väike Emajõgi, Õhne, Tarvastu, and Tänassilma rivers are the largest inflows. Suur Emajõgi is the single outlet; however at times in spring when dammed up by a mighty flood from the Pede River 5 km downstream, the river starts flowing back towards the lake. During such a period (on the average two weeks a year) Lake Võrtsjarv is devoid of any outflow. As a result, the high waterlevel usually lasts for several months in spring, while even the rise in autumn can be noticeable. The mean annual difference in the lake volume between the high and low water level can be threefold.
A permanent current system in the lake is lacking.
The lake is covered with ice on the average for 135 days a year, from the end of November till the end of April. The average water temperature rises up to 17-21°C in July. No permanent stratification occurs in summer. Võrtsjärv is a strongly eutrophic lake. The nutrients, nitrogen and phosporus issue from the surrounding arable lands and, with sewage, from several small towns (Valga, Viljandi, Tõrva) and villages. The fast expansion of reed thickets and the deterioration of biological diversity are a clear evidence of the eutrophication of the lake during the last decades. However, the high carbonate content of water protects the lake against acid rains. Due to the prevalence of western winds, the reed belt is continuous and lush on the sheltered western shore and broken at the open eastern one. The narrow southern end, especially beginning from Pähksaar Island is totally overgrown with yellow and white lilies, pondweeds, arrowhead, bulrush, and other water plants.
The amount of planktonic algae can reach 30g per cubic metre, with blue-green algae prevailing in summer. Water is turbid, yellowish-green or greenish yellow, with a transparency of about 1m. Mud particles stirred up by the wave action contribute to turbidity. The zooplankton of the lake consists of smaller animals building up the summer biomass of about
1-2 rt g/m3. The amount of bottom animals is low but variable in different years; the average biomass is 5-7 g/m2, with chironomid larvae being the dominating group.
About 35 fish species occur in Lake Võrtsjärv. Pike-perch, eel, bream and pike are the most important commercial fishes, while perch and roachare are also abundant. In the fifties and sixties Võrtsjärv was known as a ruff lake since inferior fish prevailed in catches. After the application of measures proposed by scientists of the Limnological Station (ban on trawling, strict fish protection, introduction of glass eels), big and valuable fish species became dominating. The negligible natural eel have been caught in some years. The total yearly fish catch averages over 400 tons in Lake Võrtsjärv, with the share of valuable fish 60-70%. The value of fish catches has grown 6-8–fold.