Palaeoecological records are required to test ecological hypotheses necessary for conservation strategies as short-term observations can insufficiently capture natural variability and identify drivers of biotic change. Here, we demonstrate the importance of an integrated conservation palaeobiology approach when making validated decisions for conservation and mitigating action. Our model system is the Razim-Sinoie lake complex (RSL) in the Danube Delta (Black Sea coast, Romania), a dynamic coastal lake system hosting unique Pontocaspian mollusc species that are now severely under threat. The Pontocaspians refer to an endemic species group that evolved in the Black Sea and Caspian Sea basins under reduced salinity settings over the past few million years. The natural, pre-industrial RSL contained a salinity gradient from fresh to mesohaline (18ppm) until human intervention reduced the inflow of mesohaline Black Sea water into the lake system. We reconstruct the evolution of the RSL over the past 2000 years from integrated sedimentary facies and faunal analyses based on 11 age-dated sediment cores and investigate the response of mollusc species and communities to those past environmental changes. Three species associations ("marine", "Pontocaspian" and "freshwater") exist and their spatio-temporal shifts through the system are documented. Variable salinity gradients developed, with marine settings (and faunas) dominating in the southern part of the system and freshwater conditions (and faunas) in the northern and western parts. Pontocaspian species have mostly occurred in the centre of the RSL within the marine-freshwater salinity gradient. Today, freshwater species dominate the entire system, and only a single Pontocaspian species (Monodacna colorata) is found alive. We show that the human-induced reduced marine influence in the system has been a major driver of the decline of the endemic Pontocaspian biota. It urges improved conservation action by re-establishing a salinity gradient in the lake system to preserve these unique species.