In this paper, the main trends of long-term (over 70 years) studies conducted by the Laboratory of Fish Ecology and Aquatic Invertebrates at the Institute of Biology of the Karelian Research Centre RAS are described and their results are reported. The Karelian science school in ichthyology and hydrobiology, well-known now in Russia and abroad, has formed in Karelia over the years of research on aquatic ecosystems. Aquatic ecosystems are Karelia’s greatest asset. The region’s hydrographic network, which consists of 21 000 rivers connecting over 60 000 lakes to form lake-river systems, is described. About 50 % of Lake Ladoga and about 80 % of Lake Onego, Europe’s largest freshwater bodies, are situated
in Karelia. Aquatic ecosystems are widely used in various types of human activities. General trends in Karelia’s aquatic ecosystems have been analyzed to better understand their functioning at all trophic levels (phyto-zooplankton, zoobenthos, and the fish component of communities) in a natural and disturbed state and to develop methods for environmental forecasting. To predict the future state of the region’s aquatic ecosystems, simulations were run under various conditions in collaboration with mathematicians and physicists. Seeking to maintain the biodiversity of the region’s aquatic ecosystems, researchers from the Laboratory contributed to the designation of protected areas of various categories. Interdisciplinary studies within some international projects and programs have been carried out for 20 years. The results obtained are widely used by various institutions and organizations in Karelia and other regions of Russia, as well as in Finland and Norway.