Despite fundamental progress in geoarchaeological research in the Austrian Salzkammergut region, there are still many unanswered questions regarding human activity and its relationship to climate change and the diverse environments during prehistoric times. A new palynological record from the varved composite sediment core MO-05 from the south-eastern part of Lake Mondsee (47°49′N, 13°24′E, 481 m above sea level) provides palaeoecological evidence of a long-term, although possibly discontinuous, Late Neolithic/Copper Age habitation around the study site between ca. 6000 and 4000 cal BP. Agricultural activity during this interval focused on animal husbandry, which had only a minor impact on the natural forest vegetation. A particularly low level of local human activity is indicated at the end of the Late Neolithic between 4200 and 4000 cal BP while palynological indicators of deforestation and agriculture show a re-increase in human activity during the Early to early Middle Bronze Age (ca. 3950–3460 cal BP). Without clear evidence of human activity in the vicinity of the coring site, the increasing agricultural activities were most likely restricted to areas more distant from Lake Mondsee. The end of the Late Neolithic/Copper Age habitation phase with evidence of animal husbandry and local fire activity at 4200 cal BP coincides with the Northgrippian–Meghalayan transition, which is marked by a gradual change in vegetation distribution expressed by a shift to lower scores of the dominant cool mixed (COMX) forest biome. This shift to a cooler and wetter climate regime might have caused the decrease in human activity around this time.