AbstractPredicting phytoplankton succession and variability in natural systems remains to be a grand challenge in aquatic ecosystems research. In this study, we identified six major plankton groups in Lake Bourget (France), based on cell size, taxonomic properties, food-web interactions and occurrence patterns: cyanobacterium Planktothrix rubescens, small and large phytoplankton, mixotrophs, herbivorous and carnivorous zooplankton. We then developed a deterministic dynamic model that describes the dynamics of these groups in terms of carbon and phosphorus fluxes, as well as of particulate organic phosphorus and dissolved inorganic phosphorus. The modular and generic model scheme, implemented as a set of modules under Framework for Aquatic Biogeochemical Models (FABM) enables run-time coupling of the plankton module an arbitrary number of times, each time with a prescribed position across the autotrophy/heterotrophy continuum. Parameters of the plankton groups were mainly determined conjointly by the taxonomic and allometric relationships, based on the species composition and average cellular volume of each group. The biogeochemical model was coupled to the one-dimensional General Ocean Turbulence Model (GOTM) and forced with local meteorological conditions. The coupled model system shows very high skill in predicting the spatiotemporal distributions of water temperature and dissolved inorganic phosphorus for five simulated years within the period 2004 to 2010, and intermediate skill in predicting the plankton succession. We performed a scenario analysis to gain insight into the factors driving the sudden disappearance of P. rubescens in 2010. Our results provide evidence for the hypothesis that the abundance of this species before the onset of stratification is critical for its success later in the growing season, pointing thereby to a priority effect.