Climate change and reduction in nutrient loads have significant effects on primary production and phytoplankton growth dynamics. Since in the last few decades in many regions, nutrients in lakes were reduced simultaneously as the climate changed. Yet, it remains unclear which of the two has impacted primary production the most. In this study, we couple the General Ocean Turbulence Model with the Ecological Regional Ocean Model to disentangle the effects of climate change and reoligotrophication on primary production (PP) in Lake Geneva, Switzerland–France. We apply a data assimilation method to calibrate the model with the observations from the past (1981–1990) and validate it against the in situ data from the present decade (2011–2019). Both decades represent different climate conditions and trophic states of the lake. We show that the model is skilful to reproduce assimilated and unassimilated observations from both periods. According to our results, the effect of reoligotrophication on PP is marginally higher than that of warming, leading to a net decrease in primary production by 10% from the past to the present. The areal phosphorus supply in Lake Geneva, in spite of a decrease by ∼70%, is still characteristic of a meso-to-eutrophic ecosystem. This points towards an incomplete reoligotrophication of the lake. The effects of future climate change on winter mixing and PP dynamics have also been studied. Although there would be a significant reduction in deep mixing, the autotrophic production in Lake Geneva is expected to increase by ∼20% by the end of twenty-first century, largely due to stimulation in biomass build-up of temperature-dependent algae (e.g. dinoflagellates and cyanobacteria). Considering our results to represent other large temperate lakes with similar trophic status and water residence time as Lake Geneva, future climate scenarios are expected to bring back symptoms of eutrophication.