Recently developed organic proxies (TEX₈₆, MBT/CBT, OH-GDGT₁₃₁₈/cren) based on glycerol dialkyl glycerol tetraether (GDGT) membrane lipids from ammonia-oxidizing Archaea (Thaumarchaeota) and Bacteria provide a unique tool to reconstruct the temperature history of the Baltic Sea region. However, factors, such as the diversity of GDGTs producers, their distribution in the water column, seasonality and water oxygen concentration may affect the interpretation of GDGTs related proxies. The geographical isolation of the Baltic Sea, its relatively small size, its particular physical and chemical properties (salinity, oxygen) and the existing long-term monitoring time-series represents a unique opportunity to study in details the functioning and application of GDGT-based proxies for brackish and redox-sensitive marginal seas. First, representative soil and river samples from the drainage basin, monthly resolved sediment trap samples, water column samples and surface sediments from the Baltic Sea will be analysed in order to better constrain the origin, season and depth of GDGTs production. Temperature experiments will also be conducted on an enrichment culture of Thaumarchaeota from the Baltic Sea. Second, short sediment cores from oxic and anoxic basins of the Baltic Sea will be analyzed to compare proxy-based temperature estimates with instrumental data over the last 50 years and to assess the potential effects of changing redox conditions and NH₄⁺ concentrations on GDGT-based proxies. Finally, in order to extend the records beyond the instrumental period and to obtain new insights on the climate variability of the Baltic Sea region over the last 2000 years at a multi-decadal to decadal timescale, GDGT-based proxies will be applied on long sediment cores together with other biomarkers. The results of this project should not only help to better understand the functioning of GDGT-based proxies in brackish and redox-sensitive marginal seas, but also shed new light on the relationships between temperature, primary production and hypoxia in the Baltic Sea case study.