The article presents information on the chemical composition and salinity of pore-waters of the Holocene bottom sediments in the shelf and limans from the Northwestern Black Sea region. The specific features of the water quality distribution laterally and in depth are considered. The peculiarities of the structure of hydrogeochemical sections confirm the transgressive-regressive character of the sea level change. Analysis of the geological structure, hydrogeochemical and paleoclimatic features allowed to substantiate the hypothesis of the use of limans as sources of salt in the Holocene period. Based on the information on the hydrochemical features of bottom sediments and changes in sea level, the reconstructions of paleogeographic sedimentation environments during the late Pleistocene-Holocene time on the northwestern shelf and limans of the Black Sea are presented.