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In this paper, we use empirical modeling to predict and understand phytoplankton dynamics in a reservoir affected by water transfers. Prediction of phytoplankton biovolume is central to the management of water resources, particularly given the significant impacts on quality of the water‐quantity oriented management of transfers between reservoirs. A novel tree‐based iterative input variable selection algorithm is applied for the first time in an ecological context, and identifies a maximum of eight driving factors out of 77 candidates to explain the biovolume of chlorophytes, cyanobacteria and diatoms. The stepwise forward‐selection to iteratively identify the most important inputs leads to a physically interpretable model able to infer the physical processes controlling phytoplankton biovolume. Reservoir inflows and outflows are found to exert a strong control over diatom and chlorophyte dynamics while water …