Changes in temperature and nutrients are considered the most important factors controlling phytoplankton composition and cyanobacterial abundance in freshwater lakes, although their relative importance and their interaction are still unclear. In this study we applied a recently developed open source 1D model GLM-FABM to two lakes (Mt Bold reservoir, AU; Lake Tarawera, NZ) with different trophic state.  After calibration and validation a matrix of 25 scenarios, combining temperature and nutrient changes during a period of two years was simulated. It was analysed how changes in physical and chemical variables affected phytoplankton abundance and composition. Additionally relative importance of temperature and nutrient and their interaction was evaluated. Modelling experiments showed that seasonal variability and trophic states affect the relative importance of these two factors. Moreover, the competition between algal groups (e.g. Chlorophytes and Cyanobacteria) was identified as a significant factor controlling the development of the phytoplankton community and its response to the external drivers.