Anthropogenic eutrophication can initiate vast and persistent ecosystem state changes in lakes. Such changes may be characterized by increased phytoplankton taxa variability, which can affect the effectiveness and time of lake recovery mechanisms. Lake Morat in Switzerland has undergone intense eutrophication in the 20th century (phosphorous concentrations up to 150 μg L-1) caused by excessive nutrient loadings from agricultural intensification and urbanization. Phosphorous reduction measures since 1986, such as the ban of phosphates in detergents and decreased use of fertilizers in agriculture, have resulted in total phosphorous concentrations up to 20 μg L-1 today. Despite this drastic reduction of total phosphorous, total biomass production stays high. We investigate historical changes in the phytoplankton community during the eutrophication and re-oligotrophication periods by comparing historical limnological data with sediment pigment concentrations measured by HPLC and other geochemical proxies in a radiodated sediment core. For the last 90 years, we identified four major trophic state changes in Lake Morat. The first period (AD 1924-1937) is characterized by low pigment concentrations and nutrient inputs, with good oxygen conditions. This section represents trophic conditions before the intensive eutrophication phase. The second period (AD 1937-1970) revealed an abrupt increase in pigment concentrations with higher primary production, cyanobacteria dominance and reduced oxygen levels. Oscillaxanthin indicated a Planktothrix rubescens dominance (AD 1954-1970) with concentrations up to 800 nmol g-1 OM. Their decline after AD 1970 suggests the initiation of an intense eutrophication phase (AD 1970-1983) associated with the dominance of other cyanobacteria species, higher total phosphorous inputs, and intense anoxia. In the restoration period (AD 1983-2014), there was a shift in the phototrophic community from cyanobacteria to green algae dominance, yet some cyanobacteria species remain present. Rapid phytoplankton community changes were identified in the studied period, yet overall primary production response was low. Limnological data revealed a delay of phosphorous reduction due to phosphorous recycling from the sediments. The observation of complex lake ecosystem reactions to prolonged eutrophication and subsequent re-oligotrophication, as shown by the paleolimnological and limnological data in this study, emphasize the importance of careful lake management to revert eutrophication back to historical reference biomass values.