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Eutrophication is a well-known problem of global proportions with some easily recognizable and potentially harmful effects on aquatic habitats, but our knowledge on the underlying associated changes in ecosystem functioning is rather limited. Relevant studies suggest that seasonal variability in the functional composition of phytoplankton shows an increase as eutrophication progresses. The aim of the present study was to test this hypothesis through the assessment of long-term changes in the functional diversity and composition of phytoplankton in a large shallow lake situated in Central Europe with a history of dramatic changes in trophic state. Contrary to our expectations, results have shown that the maximum range of compositional variability had a significant negative correlation with the summer biomass maxima. On the other hand, average seasonal variability measured as annual beta diversity exhibited an increasing trend throughout the years from the period of early eutrophication to the recent period of reoligotrophication, seemingly following a decline in functional richness and a long-term rise in annual mean water temperature. The enhanced variability in phytoplankton succession implies that all the ecosystem processes connected to the phytoplankton follow more complex seasonal dynamics. Besides changing community structure, trophic state also seems to be an important factor in setting the limits to compositional changes during the annual cycle, whereas long-term warming is likely to enhance instability in the phytoplankton. The trajectories of these two factors and the changes in seasonal succession indicate a lake in transition, urging more in-depth research efforts to understand the impact of climate change on this specific ecosystem, and raise the question of whether the observed changes can also occur in other similar aquatic systems.