The climate is expected to become warmer and wetter in many temperate regions and is expected to affect the water quality in lakes and reservoirs. In this paper, we investigate the impacts of a regional climate scenario on lake productivity using three models in sequence and quantify the response in biomass of three phytoplankton groups. We used a watershed model (GWLF), a physical lake model (PROBE), and a phytoplankton model (PROTBAS) for simulations of a large (61 km2), shallow (mean depth 3.4 m), wind-exposed lake basin with a short water retention time (1 month) at the western end of Lake Mälaren, Sweden. The results suggest that a future scenario with increased warming leads to a longer growing season for phytoplankton, slightly increased levels of total biomass, and a distinct shift in phytoplankton groups to favor nitrogen-fixing cyanobacteria at the expense of diatoms in this lake basin. The changes in the timing of nutrient export from the catchment are the primary cause of cyanobacteria dominance over diatoms, and elevated lake temperatures are responsible for the increase in total phytoplankton biomass.