This paper examines the archaeological settlement pattern and vegetation history of Bela krajina region of Slovenia in order to better understand the interaction of human activities and environmental processes in the landscape. Pollen record of two small palaeoecological sites (Mlaka and Griblje) indicates that human impact on the vegetation at circa 4150 calBC was intensive (forest cutting/burning, beech decline and formation of fields, pastures, meadows) and can be associated with numerous Neolithic/Eneolithic sites, located in the Lahinja river basin and the Kolpa lowlands. Human pressure on the (lowland/riverine) environment slightly decreased between c. 3750–2850 calBC. This coincides with the appearance of a more dispersed settlement pattern, including the formation of short-term settlement/activity areas on the karst plateau. This change to a more extensive Eneolithic settlement pattern can be presumably associated with change in economy (more intensive pastoralism and transhumance, possibly also soil erosion) and is partially borne out by evidence from excavated sites in the area.