Abstract Climate warming and legacy phosphorus (P) in sediments are two main factors counteracting current efforts to prevent eutrophication of temperate freshwater lakes and reservoirs. Climate warming impacts lacustrine thermal regimes, accelerates harmful cyanobacterial growth, and increases the probability of periodic anoxic bottom conditions. Legacy P in sediments becomes influential over eutrophication because of its reactivation under anoxic conditions. Lake Stechlin is a deep glacial lake of the Baltic Lake area, Germany in which artificial external P loading has been effectively blocked for more than 3 decades. The lakes trophic status was oligotrophic, until roughly 2 decades ago when it accelerated toward higher trophic levels. Here we analyse the temporal dynamics of Lake Stechlin phytoplankton biomass and composition in relation to chemical and hydrological covariates, based on monitoring data from 1994 to 2019 at sampling frequency of c. 27 samples per year. Our results show an assemblage change toward cyanobacterial dominance that took place at several temporal scales. Intra‐annual compositional change became more pronounced over the study period, mainly because of changes during the autumn and winter seasons. Results from a structural break point analysis of the phytoplankton time series with covariates, and from a hierarchical cluster analysis show that major changes occurred in 2007–2011. An analysis of early warning indicators did not unambiguously support this period as a critical transition. The change rather occurred as a rapid succession of major events during these years. Results from convergent cross‐mapping causality tests are consistent with the hypothesis that increasing relative water column stability may drive eutrophication, and additionally, that the intra‐annual timing of the biomass change plays an important role in the lakes P loading. Although quantitative data on internal P loading are unavailable, internal P mobilisation from sediments appears to be the most plausible mechanism behind the increased phytoplankton biomass. Lake Stechlin, therefore, is an example of the challenges that legacy P poses to the management of freshwater ecosystems in the context of climate warming, even when external P sources are effectively blocked, and local protective measures are in place.
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