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It is well-known that recent climatic changes have strongly affected aquatic ecosystems. In this study, we examined the complex factors determining the development of phytoplankton communities during the vegetative growth season in eutrophic lakes located in a temperate zone in eastern Poland. Our analysis enabled us to divide the data into two different periods: years with a cold winter and low total precipitation, and those with a mild winter and high total precipitation. The analysis showed that the soluble and total nitrogen content, concentration of chlorophyll a, total phytoplankton biomass, and biomasses of Cyanobacteria and Cryptophyceae were significantly higher in the vegetative growth season in the year after a mild winter, whereas the soluble and total phosphorus content and phytoplankton biodiversity were significantly lower in these years. Hence, climate warming indirectly led to the loss of biodiversity in the phytoplankton communities in the studied lakes of temperate zone. During this study, we also tested the effects of increases in air temperature and total precipitation on phytoplankton communities over short time periods (14 and 28 days). The results showed that the total phytoplankton biomass and the chlorophyll a concentration were only positively correlated with the air temperature. All of the features described in this study showed how sensitive lake ecosystems are to climatic fluctuations.