•Combination of different dating methods provides robust and accurate chronology.•Varve microfacies structure reflects sedimentation conditions.•Rapid ecological shifts were caused mainly by anthropogenic pressure.•Lake water level was affected by climate change and human activity. Sediments from Lake Lubińskie, western Poland, were investigated to determine the limnological responses to environmental changes during the last 3,000 years. To identify the mechanisms driving the eutrophication in the lake, we distinguished six lithozones along with five major varve microfacies. An age-depth model based on varve counting and radiometric measurements was established resulting in final age of 946 +113/-144 before the Common Era at the bottom of the composite profile. Varve microfacies as well as geochemical, pollen, and diatom data was used to determine major phases of landscape and lake ecosystem transformations. Our data shows that until the 4th century of the Common Era, conditions in the lake were stable. Several shifts occurred before the first millennium, when changes were observed in every proxy as a response to the increased agricultural activity in the area as well as climate fluctuations. The highest frequency of shifts was observed from the 17th century onward and mirrored further deforestation (decrease in arboreal pollen), accelerated erosion (increase in Ti), increased nutrient delivery (increased total nitrogen content), and better ventilation of the water body (higher Mn/Fe ratio). Simultaneously, the lake became more eutrophic as a response to changes in the lake catchment area. Our study suggests that inferred lake-level changes are primarily related to human activity in the catchment area.