The sinkholes along the Dead Sea (DS) shores form by dissolution of an 11–10 kyr old subsurface salt layer (hereafter named the ‘Sinkholes Salt’) that precipitated on the lake’s floor during periods of negative water balance, water level decline and salinity increase. We analyze the variations in absolute elevation and thickness of this layer in 40 boreholes along the western shores of the DS, reconstruct water-body stratification, past lake levels, and paleo-bathymetry during salt deposition, and comment on the role of the salt-layer elevation in future sinkhole formation. In the northern basin of the DS, maximum thickness of salt (~ 23 m) is found where salt top and bottom elevations are below ~ 440 meters below sea level (mbsl) and ~ 465 mbsl, respectively. Above these elevations the salt layer gradually thins out until 416 mbsl, above which it is no longer found. These relationships suggest that thermohaline stratification, with a thermocline at 25–30 m depth, similar to the present day dynamics of the DS, developed annually during the salt-precipitation period, giving rise to uniform salt accumulation below the thermocline and partial to full dissolution above it. Salt accumulation was controlled by the bathymetry of the lake and its configuration relative to the thermocline, and locally hampered by discharge of subaqueous under-saturated groundwater. The truncation of the salt layer at elevation of 416 mbsl is attributed to salt dissolution down to this elevation by a relatively diluted upper water layer that developed following inflow of fresh surface water at the end of the salt period. This event also marks the change to a positive water balance and lake level rise from its lowest stand of ~ 405 mbsl, as determined from limnological considerations.