The history of the civilizations of the oases of Bukhara and Qaraqöl (southeastern Uzbekistan) since the Neolithic in relation to environmental changes is studied by the French/Uzbekistan Archaeological Mission in Bukhara 1 following pioneering Russian studies 2. Using a methodology tested in Afghanistan, the geoarchaeological side of the program focused on the drawing of a regional geomorphological map then on the identification, mapping and dating of the paleochannels of the river Zerafshan. We established the chronology of several generations of fluvial channels in relation to archaeological settlements of different eras (Early Neolithic, Neolithic, Bronze Age, Iron Age and Islamic period) and with optically stimulated luminescence dating of alluvial deposits. Based on preliminary results of these OSL dates we propose and discuss a regional environmental reconstruction. We hypothesize that the main cause of avulsion could be catastrophic floods generated by collapse of natural dams in the upper part of the Zerafshan River.