Global warming scenarios foresee increases in air temperatures of 3-5 °C in Northern European regions within the next 70 years. To evaluate the potential effects of global warming on shallow eutrophic lakes, a flow-through experiment combining three temperature scenarios and two nutrient levels was conducted in 24 outdoor mesocosms. Eight mesocosms were unheated and acted as controls, while sixteen were heated - eight according to the Intergovernmental Panel on Climate Change's (IPCC) climate scenario A2 down-scaled to regional level (2.5-4.4 °C, depending on season) and eight according to scenario A2+ with an additional 50% temperature increase. Half of the mesocosms were enriched with nitrogen and phosphorus to simulate increased runoff from terrestrial sources due to the increased precipitation predicted by the A2 scenario. The other half were un-enriched and received only natural nutrient input from the groundwater that fed all the mesocosms. The abundance and development pattern of the microbial communities within the mesocosms were tracked during a 16-month period. Generally, the results showed that the abundances of picoalgae, bacteria and heterotrophic nanoflagellates changed in a similar manner over time; abundances being lower in winter than in summer. Warming in itself had no effect on abundance, albeit it significantly modified the positive effect of the nutrients. Only at ambient temperatures did the whole microbial assemblage respond positively to nutrients. In the A2 scenario, only picoalgae responded to nutrients, while in the A2+ scenario all but the heterotrophic nanoflagellates showed a response. Elevated winter temperatures seemed not to be more important for the microbial assemblage than elevated summer temperatures. Our results demonstrate that the direct effects of warming were far less important than the nutrient effect. The results furthermore reveal that warming and nutrients in combination set off complex interactions. In consequence, global warming may possibly have pronounced effects on aquatic ecosystems if accompanied by increased nutrient loading.