The results of long-term studies of zooplankton in more than 900 lakes and rivers of the Republic of Karelia are summarized (in the drainage basins of L. Onega, the northern part of L. Ladoga, the White Sea). Many research institutes of the Karelian Republic and North-West Russia took part in the research. The main directions of zooplankton studies in lake and river systems, including basic and applied research, and evaluation of changes in the communities under the influence of natural and anthropogenic factors are considered. The topical tasks for the study of zooplankton in water bodies of Karelia are highlighted.