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We used HPLC to identify and quantify pigments in a Holocene sediment record from large, shallow Lake Peipsi, Estonia. The aim of our study was to track the influence of long-term climate change (i.e. temperature fluctuations) on past dynamics of aquatic primary producers. Sedimentary pigments were separated and quantified in 182 samples that span the last ca. 10,000 years. There was an increasing trend in sedimentary pigment concentrations from basal to upper sediment layers, suggesting a gradual increase in lake trophic status through time. Using additive models, our results suggested that primary producer dynamics in Lake Peipsi were closely related to temperature fluctuations. We, however, identified two periods (early Holocene and after ca. 2.5 cal ka BP) when the relationship between primary producer composition and temperature was weak, suggesting the influence of additional drivers on the primary producer community. We postulate that: (a) the increase of primary producer biomass in the early Holocene could have been caused by input of allochthonous organic matter and nutrients from the flooded areas when water level in Lake Peipsi was increasing, and (b) changes in the abundance and structure of primary producer assemblages since ca. 2.5 cal ka BP was related to widespread agricultural activities in the Lake Peipsi catchment. These results suggest that human activities can disrupt the relationship between the primary producer community and temperature in large, shallow lakes.