Abstract The origin of hypersaline brines from Urania and Bannock deep anoxic basins in the eastern Mediterranean Sea has been investigated by integrating geochemical data and boron isotopic ratios. Bottom brines from Urania basin have chloride contents up to 4200 mmole/kg H 2O and a marine Na/Cl ratio (0.87). All the other ionic ratios are different from the marine ratios and show a relative enrichment in Ca, K, Br, and B and depletion in Mg and SO 4, as normalized to the chloride ion. The δ 11B values of the Urania brines (δ 11B = 29.8 ± 2.9‰; n = 7) are lower than that of Mediterranean seawater (39‰). The concentrations of Cl and Na, which make up 95% of the total dissolved ions (in molal units), suggest that the Urania brines were derived from eightfold evaporated seawater. The relative enrichment of Ca and depletion of Mg and SO 4 reflect dolomitization, gypsum precipitation, and sulfate reduction processes which modified the original evaporated seawater while the brines were entrapped as interstitial waters in the sedimentary section of the Mediterranean. The relative enrichments of Br, B, and K, and the low δ 11B value of the Urania brines suggest high-temperatures interactions of the evaporated sea water with sediments. Mass-balance calculations suggest that desorption of exchangeable B from the sediments (δ 11B ∼ 20‰) modified the marine B isotopic composition of the original eightfold evaporated seawater. Potassium was also leached from clay minerals whereas Br was contributed from degradation of organic matter in the sediments. This is consistent with a thermal anomaly (up to 45°C) recorded at depth in the region of Urania basin. In contrast, bottom brines and shallow interstitial fluids from Bannock basin with low temperatures (15°C) show marine δ 11B (δ 11B = 39.6 ± 2.8‰; n = 5; 38.5 ± 2.2‰; n = 5, respectively) and B/Cl ratios (7 × 10 −4). The B isotope data confirm that the Bannock brines were derived from twelvefold evaporated seawater. We argue that the brines from both basins are relics of fossil evaporated seawater that was entrapped in Late-Miocene sediments and accumulated in the deep basins of the Mediterranean seafloor.