Restricted basins, such as the Baltic Sea, are particularly affected by global warming, which leads to intensifying stratification, severe oxygen depletion and increasing water temperatures. This, in turn, results in significant and lasting ecosystem alterations. Sediment cores recovered during IODP Expedition 347 allow reconstructing such changes. We analysed Holocene sediments from the Landsort Deep (IODP Site M0063) using combined palynological and biogeochemical approaches to reconstruct palaeoclimate variations as well as ecosystem changes and to identify anthropogenic influences. Comparison of pollen data with organic-walled dinoflagellate cysts and other palynomorphs provides a direct land-sea comparison, while increasing palynomorph concentrations are indicative for dysoxic conditions and better preservation. Our results indicate particularly warm conditions (based on TEX86) that are paralleled by high primary productivity (high TOC) and increased anoxia (low pristane/phytane ratios) around the Holocene Thermal Maximum (~7 to 5 kyr BP), Medieval Climate Optimum (~1 kyr BP) and Modern Hypoxic Period (since ~1950). For the late to middle Holocene (~7 to ~4 kyr BP), our data imply a decreasing brackish-marine influence until 4 to 3 kyr BP, accompanied by diminished aquatic primary productivity indicated by declining abundances of dinoflagellate cysts and an increase of the terrestrial vs. aquatic ratio (TARHC). Our data do not reveal equally strong terrestrial ecosystem changes until the past ca. 1000 years, which witnessed increased agricultural activity, implied by higher abundances of rye pollen as well as probably anthropogenically induced deforestation, implied by a relative decrease in non-saccate tree pollen and increase in non-arboreal pollen.