Climate change has increased the frequency, duration and intensity of heatwaves in Europe. These extreme events result in alterations of physical, chemical, and biological properties of lakes that may synergistically promote cyanobacterial dominance. In our study we focused on cyanobacterial blooms in lakes distributed over a longitudinal gradient in Central Europe during one of the “top ten European heat waves” in summer 2015. 92 lakes were included in the study, located across three climatic subregions: cool northern lakes, situated in Lithuania, temperate northern lakes in Poland, and warm northern lakes in Croatia. The objective of the study was to determine if cyanobacterial biomass, predominant species, and cyanotoxin concentration differed, across the south-north gradient, as a function of water temperature, total phosphorus, and total nitrogen. Statistical significance of observed patterns was tested using the Kruskal-Wallis rank sum test and the generalized linear model. We found the lowest average epilimnion temperature, but the highest average cyanobacterial biomass in the northern, ‘cool’ lakes while the highest average temperature with the lowest average cyanobacterial biomass in the southern, ‘warm’ lakes. The concentration of cyanotoxins was also the highest in the ‘cool’ lakes. Total phosphorus and total nitrogen correlated significantly with cyanobacterial biomass, cyanotoxins concentration and biomass of some cyanobacterial species (mainly Planktothrix agardhii), regardless of the latitude. Only in the ‘cool’ lakes concentration of cyanotoxins (microcystins and anatoxin-a) correlated significantly with cyanobacterial biomass and the biomass of some dominant cyanobacterial species (P. agardhii). Our results emphasized the differences of heat weaves impact on lakes of various latitudes, with the strongest increase in toxic cyanobacterial blooms in northern ‘cool’ lakes, situated in high latitudes. On the other hand, nutrients directly enhanced blooms across all the studied latitudes of Central Europe. The cyanobacteria species dominating in blooms might be recognized as ecological indicators of climate change, especially in the north-eastern part of Europe.