The Eastern Mediterranean Sea lies in a climatological transition zone, under the influence of both tropical and mid-latitude climate processes. Within this basin, the Aegean Sea has been recognized as a highly sensitive area to global/regional climate change. Sediment archives provide robust evidence for changes in its hydrological properties and biogeochemical functioning as a response to past climate variability. In order to investigate the region's paleoclimatic and paleoceanographic patterns during the Holocene, with a special emphasis on the sapropel S1 interval, we have investigated marine sediment cores along a N-S transect in the Aegean and the S. Cretan Seas. We focus on combined geochemical, micropaleontological and palynological proxies, namely organic biomarkers, organic carbon and nitrogen stable isotopes, coccolithophore and pollen assemblages, aiming at reconstructing climate-related parameters such as sea surface temperature (SST), marine productivity patterns, stratification and nutricline fluctuations, continental vegetation patterns and land-sea interactions. SST patterns depict major global/regional climate fluctuations during the last glacial and deglaciation periods, depict the warm transition to the Holocene optimum, when the formation of the S1 sapropel takes place, a distinct cool episode around 8 ka BP (coeval with the S1 interruption), a conspicuous mid-Holocene warm phase (5.4-4.3 ka BP) as well as other distinct fluctuations. Diagnostic marine lipids, δ¹⁵N, and coccolithophore assemblages allow documenting the variability of primary productivity and associated organic carbon accumulation in sediments, as well as fluctuations in water column stratification and nutricline, especially during the deposition of the S1 sapropel. Combined terrigenous proxies record warm/cool and dry/humid time intervals, allowing land-sea correlations, and document changes in the delivery of terrestrial material to the sea related to climate-driven fluctuations in freshwater discharges. The network of sediment cores studied provide a better constrain of the regional climate patterns in the northeastern Mediterranean Sea and enables assessing potential time lags and gradients.