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Understanding the long-term dynamics of ecological communities on the centuries-to-millennia scale is important for explaining the emergence of present-day biodiversity patterns and for predicting possible future scenarios. Fossil pigments and ancient DNA present in various sedimentary deposits can be analysed to study long-term changes in ecological communities. We analysed recent compilations of data, including fossil pigments, microfossils, and molecular inventories from the sedimentary archives, to understand the impact of gradual versus abrupt climate changes on the ecosystem status of a regional model lake over the last ∼14.5 kyr. Such long and complete paleo-archives are scarce in North-Eastern Europe. The study site lies in a sensitive area, both climatically and in respect to vegetation. Namely the maritime-continentality line runs west to east in the central Baltic area to NE Europe and its south-north transect lies within the gradual decay of the nemoral forest into a boreal environment. Therefore, the selected location is an ideal sampling point to decipher long term environmental changes in the temperate climate zone. The main objective of the present study was to find out external factors influencing phototroph dynamics at temperate Lake Lielais Svētiņu over the post-glacial period (∼14.5 kyr). We were able to model climate change together with vegetation change and the appearance of anthropogenic forcing, either as a gradual change or as abrupt events that influenced the phototrophs, which are keystone groups within the lacustrine ecosystem. Most interestingly, the gradual increase of species richness of phototrophs was linked to similar increase in fungal parasites of the same group – phototrophs. Abrupt climate change in the Late Glacial period caused abrupt events in the ecosystem but equally abrupt events were caused by gradual changes during the stable period of the Holocene Thermal Maximum (HTM). In addition, we highlight the increased frequency and degree of perturbation in pristine lakes due to low impact human activity over a larger region. Both observations demonstrate an impaired relationship between gradual external drivers and ecosystem response and apply to future scenarios of climate warming and increased human impact in north-eastern Europe. • Gradual climate change leads to natural eutrophication or oligotrophication processes depending on whether the climate is warming or cooling. • A threshold-like response of the phototroph community occurs when climate, lake ontogeny or human influence disrupts the in-lake community. • Low impact disruption can lead to increased microbial biodiversity in aquatic ecosystems, most prominently in fungal parasites of phototrophs, which could lead to future non-linear changes in lake ecological status. [ABSTRACT FROM AUTHOR]