87Sr/86Sr isotope and Sr/Ca ratios in lacustrine carbonates were used to reconstruct the hydroclimate conditions in the watershed of Lake Bira that filled during the Tortonian-Messinian the tectonic depressions of the Northern Valleys of Israel in the East Mediterranean-Levant region. 87Sr/86Sr ratios of the Tortonian (ca. 10–8 Ma) carbonates of ∼0.7075 and the great expansion of the lake indicate wet conditions and enhanced supply of freshwater from the regional Mesozoic aquifers. Upon the transition to the Messinian period (ca. 7–6 Ma), the 87Sr/86Sr ratios in the carbonates rose to ∼0.7080–0.7085, reflecting the contribution of Sr from Sahara Desert dusts that came to comprise the regional surface cover. This contribution is also reflected in the silicate fraction of the lacustrine formations that show “granitic-crustal” 87Sr/86Sr ratios of ∼0.711. During the Messinian salinity crisis (5.9–5.6 Ma), the region became arid and Lake Bira possibly dried. Later, during the Lago Mare stage (ca. 5.5–5.3 Ma), the rainfall increased and paludal waterbodies scattered the area of the larger Lake Bira.