Lakes Samra, Lisan and the Dead Sea occupied the Dead Sea basin during the Last Interglacial (not, vert, similar140–75 ka BP), last glacial (not, vert, similar70–14 ka BP) and Holocene periods, respectively. The age of Lake Lisan and Samra was determined by U–Th dating of primary aragonites comprising parts of the lacustrine sedimentary sequences. The lakes have periodically deposited sequences of layered calcitic marls (Lake Samra) or laminated primary aragonite (Lake Lisan). The deposition of aragonite as the primary carbonate phase reflects the contribution of the incoming freshwater (loaded with bi-carbonate) and high Mg-, Ca-chloride brine that originated from the subsurface vicinity of the Dead Sea basin. Deposition of calcitic marls suggests a minor effect of the brines. The Ca-chloride subsurface brine has been migrating in and out of the wall rocks of the Dead Sea basin, reflecting the regional hydrological conditions. During most of the last glacial period and during the late Holocene, sufficient precipitation above the Judea Mountains pushed the subsurface Ca-chloride brines into the lakes causing the deposition of aragonite. During the Last Interglacial period the rain that precipitated above the Judea Mountains was insufficient to induce brine flow toward Lake Samra. It appears that sporadic floods provided calcium, bicarbonate and detritus to produce the Samra calcitic marls. Travertines deposited at the Samra–Lisan boundary indicate the early stage in the resumption of groundwater (springs) activity that led to the resurgence of Ca-chloride brine and rise of Lake Lisan. Similar variations in the regional rain precipitation and hydrological activity probably characterized the long-term geochemical evolution of Pleistocene lacustrine water-bodies in the Dead Sea basin, enabling the use of the carbonates as paleo-hydrological monitors.