The lake was previously part of Lake Lisan and reached its highest level in the Upper Paleolithic around 12,000 BC of 100 metres below sea level when it was included the area that is now Lake Tiberius (The Sea of Gallilee) and extended south as far as Wadi Yabis and Wadi Malih. It was first noticed by Dr. Leo Picard in a publication of 1929 who noticed higher altitude lake beds and eroded rock structures and named the lake after a notable ancient town in the area. David Neev conducted stratigraphic analysis in 1967 to provide further evidence from a sequence of sediments left by the lake.
Archaeological evidence supports the geological with no epipaleolithic sites on the western side of the Beisan Basin below 100 metres below sea level. During the neolithic, the lake receded to approximately 200 metres below sea level due to erosion and formation of the Jordan river and an arid phase that peaked around 8500 BC. This was followed by a wetter and warmer phase between 7500 and 6500 BC where the population increased significantly and the receding lake gave way to agriculture. Later in the neolithic the climate became dryer and the lake further retreated to around 220 metres below sea level between 6500 and 5500 BC as the flow through the Jordan Valley reduced. After this, in the chalcolithic period it turned into a swamp with a possible shallow lake forming in winter. This left flood plains into the early Bronze Age when settlements intensified on the eastern side of the basin. The Jordan river gradually deepened sufficiently for all remnants of the lake to have disappeared by the time of the middle Bronze Age.
- Smith R. H. & Koucky F. L., Lake Beisan and the Prehistoric Settlement of the Northern Jordan Valley, Paléorient, Volume 12, Issue 12-2, pp. 27-36
- Leo Picard (1929). Zur Geologie der Bēsān-Ebene. J. C. Hinrichs. Retrieved 13 April 2011.
- David Neev; Kenneth Orris Emery (1967). The Dead Sea: depositional processes and environments of evaporites. Ministry of Development Geological Survey of Israël. Retrieved 13 April 2011.