Phosphorus (P) precipitation is among the most effective treatments to mitigate lake eutrophication. However, after a period of high effectiveness, studies have shown possible re-eutrophication and the return of harmful algal blooms. While such abrupt ecological changes were attributed to the internal P loading, the role of lake warming and its potential synergistic effects with internal loading, thus far, has been understudied. Here, in a eutrophic lake in central Germany, we quantified the driving mechanisms of the abrupt re-eutrophication and cyanobacterial blooms in 2016 (30 years after the first P precipitation). A process-based lake ecosystem model (GOTM-WET) was established using a high-frequency monitoring data set covering contrasting trophic states. Model analyses suggested that the internal P release accounted for 68% of the cyanobacterial biomass proliferation, while lake warming contributed to 32%, including direct effects via promoting growth (18%) and synergistic effects via intensifying internal P loading (14%). The model further showed that the synergy was attributed to prolonged lake hypolimnion warming and oxygen depletion. Our study unravels the substantial role of lake warming in promoting cyanobacterial blooms in re-eutrophicated lakes. The warming effects on cyanobacteria via promoting internal loading need more attention in lake management, particularly for urban lakes.