Abstract. Lakes Prespa and Ohrid, in the Balkan region, are considered to be amongst the oldest lakes in Europe. Both lakes are hydraulically connected via karst aquifers. From Lake Ohrid, several sediment cores up to 15 m long have been studied over the last few years. Here, we document the first long sediment record from nearby Lake Prespa to clarify the influence of Lake Prespa on Lake Ohrid and the environmental history of the region. Radiocarbon dating and dated tephra layers provide robust age control and indicate that the 10.5 m long sediment record from Lake Prespa reaches back to 48 ka. Glacial sedimentation is characterized by low organic matter content and absence of carbonates in the sediments, which indicate oligotrophic conditions in both lakes. Holocene sedimentation is characterized by particularly high carbonate content in Lake Ohrid and by particularly high organic matter content in Lake Prespa, which indicates a shift towards more mesotrophic conditions in the latter. Long-term environmental change and short-term events, such as related to the Heinrich events during the Pleistocene or the 8.2 ka cooling event during the Holocene, are well recorded in both lakes, but are only evident in certain proxies. The comparison of the sediment cores from both lakes indicates that environmental change affects particularly the trophic state of Lake Prespa due to its lower volume and water depth.