Cross-latitude studies on lakes have a potential to predict how global warming may cause major changes in phytoplankton biomass and composition, e.g., the development of favourable conditions for cyanobacteria dominance. However, results from these studies may be influenced by biogeographical factors, and the conclusions may, therefore, not hold when considering local response patterns. We used monthly monitoring data from 504 lakes in Denmark-a small and homogeneous geographical region-to establish empirical relationships between key phytoplankton groups and a set of explanatory variables including total phosphorus (TP), total nitrogen (TN), lake mean depth (DEP) and water temperature (TEMP). All variables had strong effects on phytoplankton biomass and composition, but their contributions varied over the seasons, with TEMP being particularly important in June-October. We found dominance of cyanobacteria in terms of biomass and also an increase in dinophytes biomass at higher TEMP, while diatoms and chlorophytes became less important. In May, however, the TEMP effect on total phytoplankton biomass was negative, likely reflecting intensified zooplankton grazing. Our results suggest that biogeographical effects are of minor importance for the response patterns of phytoplankton to temperature and that substantial concentration reductions of TN and TP are needed in eutrophic lakes to counteract the effect of the climate change-induced increase in TEMP.