The anticipated long-term rise in temperature can have numerous effects on freshwater phytoplankton, however, there is a great deal of uncertainty about how biogeochemical processes modify community functioning under a warming climate. Previous works regarding a large shallow lake and a mesocosm study showed a positive relationship between the temporal variability of phytoplankton composition and mean temperature, which might be a sign of warming-stimulated instability in ecosystem processes. To elucidate whether these observations are part of a more general phenomenon, we combined a numerical model describing the dependence of algal growth on temperature and nutrient concentration with a multispecies, multi-nutrient model. We ran simulations representative of changes in phytoplankton communities with randomized initial species composition under different temperature scenarios (current annual temperature pattern increased with 1°C, 2°C, or 3°C), various levels of nitrogen and phosphorus supply and different degrees of temporal variability in those supplies. The model outputs showed that seasonal variability in composition can be enhanced by warming through the mechanistic links between nutrient availability, temperature, and species-specific growth rates, but the rate of increase is also dependent on nutrient ratios and the size of the species pool. Moreover, temporal variability in nutrient loads also enhanced compositional variability, but the rate of increase also depended on the level of nutrient supply. The results of our study hint that the impact of climate change and eutrophication on phytoplankton dynamics can be more intricate than spatiotemporally limited field or experimental observations would suggest.