Regional climate change scenarios predict increased temperature and precipitation in the northern Baltic Sea, leading to a greater runoff of fresh water and terrestrial dissolved organic carbon (DOC) within the second part of the 21st century. As a result, the current north to south gradient in temperature and salinity is likely to be shifted further toward the south. To examine if such climate change effects would cause alterations in the environmental fate of organic pollutants, spatial variations of DOC quality and sorption behavior toward organic contaminants were examined using multiple analytical methods. The results showed declining contents of aromatic functional groups in DOC along a north to south gradient. Similarly, the sorption of a diverse set of organic contaminants to DOC also showed spatial differences. The sorption behavior of these contaminants was modeled using poly parameter linear energy relationships. The resulting molecular descriptors indicated clear differences in the sorption properties of DOC sampled in northern and southern parts of the Baltic Sea, which imply that more organic contaminants are sorbed to DOC in the northern part. The extent of this sorption process determines whether individual contaminants will partition to biota via direct uptake or through sorption to DOC, which serves as food source for bacteria-based food-webs.