In the densely forested Warmia and Masuria region (northern Poland) there are many small endorheic lakes characterized by their low sedimentation rate, which makes them excellent archives of Holocene environmental and palaeoclimatic change. Lake Młynek, located near the village of Janiki Wielkie, was selected for multi-faceted palaeoenvironmental research supported with radiocarbon dates. Sediments from this lake also contain unique information about human impact on the environment, because a stronghold has been operating on its northern shore since the early Iron Age to the early Medieval period, giving the opportunity to correlate palaeoenvironmental data with the phases of human activity over the last 2400 years. During the second and third centuries BCE the lake was surrounded by a dense deciduous forest. From the first century BCE to second century CE the forest around the lake was much reduced, which can be associated with the first pre-Roman (La Tène) and Roman occupation phase evidenced by the construction of the stronghold located close to the lake. From the second up to ninth century CE gradual restoration of the forest and a decline in human activity took place, along with lake deepening and the onset of a colder and humid climatic phase which corresponded to the global cooling episode known as the Bond 1 event (1.5 ka BP). The next intensive phase of forest clearing around the lake occurred between the 9th–13th century CE as result of human activity (Middle Age settlement phase of the stronghold). Whilst this period is marked by a warming, the human impact which has transformed the landscape likely overprints any signals of climate-driven environmental changes.