In a medium-sized pre-alpine lake (North Italy) the cyanobacterium Planktothrix rubescens has strongly dominated the phytoplankton assemblage since 2000, similar to many pre-alpine lakes, despite improvements in water quality. The objective of this study was to determine the factors governing the spatial distribution of P. rubescens, including the major hydrodynamic processes and the influence of long-term reduction in nutrient concentrations during a period of climate warming. We used an intensive field campaign conducted from February 2010 to January 2011, to evaluate distributions of phytoplankton phyla, as well as P. rubescens, using spectrally resolved fluorescence measurements. These data provided highly spatially and temporally resolved phytoplankton population data suitable to calibrate and validate a coupled three-dimensional hydrodynamic (ELCOM) and ecological model (CAEDYM) of the lake ecosystem. The simulations revealed the fundamental role of physiological features of P. rubescens that led to observed vertical patterns of distribution, notably a deep chlorophyll maximum, and a strong influence of lake hydrodynamic processes, particularly during high-discharge inflows in summer stratification. The simulations are used to examine growth-limiting factors that help to explain the increased prevalence of P. rubescens during re-oligotrophication.