Deoxygenation affects many continental shelf seas across the world today and results in increasing areas of hypoxia (dissolved oxygen concentration ([O2]) <1.4 ml/L). The Baltic Sea is increasingly affected by deoxygenation. Deoxygenation correlates with other environmental variables such as changing water temperature and salinity and is directly linked to ongoing global climate change. To place the ongoing environmental changes into a larger context and to further understand the complex Baltic Sea history and its impact on North Atlantic climate, we investigated a high accumulation-rate brackish-marine sediment core from the Little Belt (Site M0059), Danish Straits, NW Europe, retrieved during the Integrated Ocean Drilling Program (IODP) Expedition 347. We combined benthic foraminiferal geochemistry, faunal assemblages, and pore water stable isotopes to reconstruct seawater conditions (e.g., oxygenation, temperature, and salinity) over the past 7.7 thousand years (ka). Bottom water salinity in the Little Belt reconstructed from modeled pore water oxygen isotope data increased between 7.7 and 7.5 ka BP as a consequence of the transition from freshwater to brackish-marine conditions. Salinity decreased gradually (from 30 to 24) from 4.1 to ~2.5 ka BP. By using the trace elemental composition (Mg/Ca, Mn/Ca, and Ba/Ca) and stable carbon and oxygen isotopes of foraminiferal species Elphidium selseyensis and E. clavatum, we identified that generally warming and hypoxia occurred between about 7.5 and 3.3 ka BP, approximately coinciding in time with the Holocene Thermal Maximum (HTM). These changes of bottom water conditions were coupled to the North Atlantic Oscillation (NAO) and relative sea level change.