Complex lake ecosystem models can assist lake managers in developing management plans counteracting the eutrophication symptoms that are expected to be a result of climate change. We applied the ecological model PCLake based on 22 years of data from shallow, eutrophic Lake Søbygaard, Denmark and simulated multiple combinations of increasing temperatures (0–6 °C), reduced external nutrient loads (0%–98%) with and without internal phosphorus loading. Simulations suggest nitrogen to be the main limiting nutrient for primary production, reflecting ample phosphorus release from the sediment. The nutrient loading reduction scenarios predicted increased diatom dominance, accompanied by an increase in the zooplankton:phytoplankton biomass ratio. Simulations generally showed phytoplankton to benefit from a warmer climate and the fraction of cyanobacteria to increase. In the 6 °C warming scenario, a nutrient load reduction of as much as 60% would be required to achieve summer chlorophyll-a levels similar to those of the baseline scenario with present-day temperatures.