The response of large water-bodies to global change in terms of ecosystem services and economical value is a major concern. The Caspian Sea, the world's largest enclosed water-body, has a poorly-known water-level history, but observed changes are a hundred times faster than recent global sea-level rise. This ancient lake, characterised by brackish waters, is rich in endemic species; some of them have spread to similar environments worldwide. However, the ecology of Pontocaspian species remains poorly understood and must be studied in their original habitat. This work aims at improving the capacity to reconstruct Quaternary environments of the Pontocaspian region and to provide a benchmark for biodiversity turnover studies. A transect of surface sediment across a wide shelf was subjected to multidisciplinary analyses: stable isotopes, pollen, dinocysts, diatoms, foraminifers, ostracods and molluscs and vertical oceanographic profiles. Three depositional environments with characteristic communities were found: shore face, shelf and slope. Invasion impact was strongly felt by the molluscs. All biota groups, except diatoms, reflected high endemism. The radiocarbon reservoir effect is highlighted in differential 14 C ages for different groups. Understanding such discrepancies require detailed insight into reworking processes. Tephra presence in the sediment shows a potential for tephrochronology. Stable isotope ratios in ostracods appear to reflect temperature depth gradients. Our results provide a baseline for calibrating proxy data to the present Pontocaspian environment.