This study was undertaken to determine the direction and extent of time related changes in the fish communities of the large shallow eutrophic lakes Peipsi and Võrtsjärv. The official statistics of commercial fisheries for the periods 1931–1940 and 1950–1999 were used for trend analysis. In the ichthyocoenosis of both lakes, several drastic and economically important changes have occurred during recent decades. Some trends in the population dynamics of fish (e.g., sharp decline of the stock of vendace Coregonus albula (L.) in Lake Peipsi) are probably irreversible owing to the eutrophication of the lake. A sharp decrease in the stock of smelt Osmerus eperlanus (L.), caused by nighttime water anoxia in the summer of several years, was followed by a quick recovery. Periodic changes in the population of pike Esox lucius L., are related to water level fluctuations. The population dynamics of several fishes, particularly pikeperch Stizostedion lucioperca (L.), are, to a large extent, controlled by fishery policy, although climatic factors are also of importance. The state of the stock of eel Anguilla anguilla (L.), depends entirely on introduction of young eels.

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