Benthic foraminiferal, sedimentological, and stable isotope analyses performed on early Zanclean sediments from Alboran Basin ODP Site 976 and southern Spanish land-based sections in the Malaga, Nijar and Sorbas basins have enabled the reconstruction of Mediterranean environmental conditions immediately after the Messinian Salinity Crisis. The presence at the Miocene – Pliocene boundary of dark layers, often enriched in organic matter, suggests that the Zanclean reflooding has created water column stratification, and reduced bottom-water oxygen levels. Considering that such dark layers are recorded at both deep and marginal settings far away from the Gibraltar gateway/s, a Mediterranean-scale water-mass stratification must have occurred. This stratification could be the result of saline Atlantic waters sinking into a less saline Mediterranean Basin still under the influence of the Paratethys. Our early Zanclean benthic δ18O data show that the Mediterranean water budget was indeed less negative than at present, explaining the lower salinity of the basin. However, the Atlantic values of the benthic δ13C registered in the Alboran basin suggest that bottom-water renewal rates were quite high during the early Zanclean, preventing the reduction of δ13C at the seafloor as observed in the Messinian records. Zanclean benthic foraminiferal repopulation sequences show similarities with recovery from low-oxic episodes during sapropel deposition. These observations, paired with the gradual deepening of the basins, suggests that the Zanclean reflooding led to a progressive shift from stressed and unstable environments towards benthic associations typical of efficient circulation and bottom water ventilation.