Nutrient loads to large, shallow Lake Balaton have been reduced by 45-50% since mid-1980s. While a delayed, but still surprisingly fast recovery was observed in the hypertrophic western areas of the lake, eutrophication followed sewage diversion from the mesotrophic northern basins. We assessed factors that could lead to this unusual response. The prime reason of the observed biomass increase might be a trend of increasing mean water temperature during late summers and the concurrent invasion of the subtropical cyanobacterium, Cylindrospermopsis raciborskii with superior light and nutrient utilisation capabilities. In the mesotrophic areas, the prerequisite of the unforeseen success of C. raciborskii was the exceptionally high potential of this species to generate internal P load. Specific morphometric features of the lake rather than nutrient loads might substantiate the increasing dominance of the cyanobacterium in these areas. Our results stress the need to consider individual characteristics of aquatic ecosystems during eutrophication management.