Zooplankton is an important element of Lake Onega ecosystem, it plays a significant role in the formation of lake biological resources and its characteristics are included in the state biomonitoring system. The study of seasonal changes in plankton became urgent due to the changes in climate and temperature regime observed in the recent decades. Mean annual characteristics of seasonal changes in the composition and structure of zooplankton are described based on the 30-year research. The relationship between seasonal changes in zooplankton structure and hydrological and temperature conditions in Petrozavodsk Bay of Lake Onega are presented.