We review the reasons for change in paleoecological conditions and their effects on different cultures at the beginning and during the Holocene period in western Hungary using radiocarbon data combined with paleoecological and paleolimnological results. Two sites were investigated in the southern and northern part of the ancient bay of Balaton Lake: Keszthely-Úsztatómajor and Főnyed I. 14C dating of 2 core samples represented a chronology from 11,000 cal BC to 2000 cal BC (10,700 BP to 3700 BP) and from 6200 cal BC to 1200 cal BC (7300 BP to 3000 BP), respectively. A relatively constant inverse sediment accumulation rate was observed in both cases (23 yr/cm and 33 yr/cm, respectively). In the case of Főnyed I, a sharp break was observed in the sedimentation curve around 6000–4800 cal BC (6000 BP). Changes in the vegetation due to human activity were observed in a larger extent only at the end of Late Neolithic, with the most significant changes detected in the landscape coinciding with the presence of Lengyel III culture in the region. The appearance of higher amounts of pollen of cereals at the sites proved the presence of crop cultivation. However, the role of plant cultivation may have been limited for the ancient inhabitants of the Kis-Balaton region due to a limited amount of soil suitable for agriculture and due to the extensive water table. Further changes in vegetation were observed during the Late Copper Age (Baden culture) and the period of Early and Middle Bronze Age, respectively. Signs of forest clearing during the period have not been detected and the increased peak of Fagus indicates climatic change. The low intensity of anthropogenic activity should not be attributed to geographic isolation.