The aim of this research was to evaluate dynamics of the zooplankton community in the middle stretch of the Daugava river over the last 50 years and the possible impact of the climate change namely variability of temperature and hydrology on zooplankton community fluctuations. Quantitative (abundance, biomass, number of taxa), qualitative (species composition) characteristics, species diversity (Shannon–Wiener index) and saprobity index (S) were employed for the analysis of zooplankton community structure in the Daugava river. For determination of zooplankton community correlated similarity Renkonen percentage similarity (Renkonen index) was used. Historic hydrological and air temperature data were analysed. A tendency for the total abundance of zooplankton and species diversity to decrease has been recorded. Relevant changes in species structure have been stated. There are also changes in the species occurrence according to seasons. Such changes could be attributed to the long-term changes in climate, namely variability of temperature and hydrology of the Daugava drainage basin.