The Skopje basin, located at the centre of the Balkan Peninsula, is a Tertiary graben with main faults still in activity. The subsiding floodplain of the Vardar River is surrounded by two ancient mountain ranges. Soft limestone hills, alluvial glacis and alluvial fans shape the foothill belt. To the north of the graben, Tumba Madzhari is currently the only Neolithic settlement recorded in the very vicinity of the floodplain. The other sites are established on Pleistocene steeped alluvial terraces and pleistocene colluvial deposits. This study aims to reconstruct the Holocene evolution of the Vardar floodplain in order to understand the geographical distribution of the Neolithic settlements in this area. Eight probes were carried out at Tumba Madzhari and down to the left bank of the Vardar River. Granulometric studies of the core sediments show high lateral mobility of the Vardar River during the Holocene period. This mobility has set since the Early Holocene the environmental background of the Neolithic colonization of the valley floor.