The aim was to investigate the impacts of climate change on the behavior of phytoplankton, with a special emphasis on harmful cyanobacteria in the peri-Alpine region. It was hypothesized that in this highly sensitive region more important episodes of harmful cyanobacteria outbreaks under warmer climatic conditions could lead to negative impacts on water quality. The objectives were i) to analyze if air temperature is able to influence the cyanobacteria community, ii) to define the main drivers for the phytoplankton/cyanobacteria community, iii) to predict the cyanobacteria biomass under warmer climatic. Multivariate analysis and statistical modeling were applied on data from seven peri-Alpine lakes. Air temperature significantly influences the phytoplankton community, which is mainly driven by nutrients and temperature. Oscillatoriales, may be favored with increased water temperature and a longer stratification period. Planktothrix rubescens biomass was projected to increase in abundance and frequency thus potentially could induce a community function change.