A Late Glacial to Holocene sediment sequence (Co1260, 717 cm) from Lake Dojran, located at the boarder of the F.Y.R. of Macedonia and Greece, has been investigated to provide information on climate variability in the Balkan region. A robust age-model was established from 13 radiocarbon ages, and indicates that the base of the sequence was deposited at ca. 12 500 cal yr BP, when the lake-level was low. Variations in sedimentological (H2O, TOC, CaCO3, TS, TOC/TN, TOC/TS, grain-size, XRF, δ18Ocarb, δ13Ccarb, δ13Corg) data were linked to hydro-acoustic data and indicate that warmer and more humid climate conditions characterised the remaining period of the Younger Dryas until the beginning of the Holocene. The Holocene exhibits significant environmental variations, including the 8.2 and 4.2 ka cooling events, the Medieval Warm Period and the Little Ice Age. Human induced erosion processes in the catchment of Lake Dojran intensified after 2800 cal yr BP.