The Scientific Collaboration on Past Speciation Conditions in Lake Ohrid (SCOPSCO) project is an international research initiative to study the influence of major geological and environmental events on the biological evolution of lake taxa. SCOPSCO drilling campaigns were carried out in 2011 and 2013. In 2011 we used gravity and piston coring at one of the five proposed drill sites, and in 2013 we undertook deep drilling with the Deep Lake Drilling System (DLDS) of Drilling, Observation and Sampling of the Earth's Continental Crust (DOSECC). In April and May 2013, a total of 2100 m sediments were recovered from four drill sites with water depths ranging from 125 to 260 m. The maximum drill depth was 569 m below the lake floor in the centre of the lake. By retrieving overlapping sediment sequences, 95% of the sediment succession was recovered. Initial data from borehole logging, core logging and geochemical measurements indicate that the sediment succession covers >1.2 million years (Ma) in a quasi-continuous sequence. These early findings suggest that the record from Lake Ohrid will substantially improve the knowledge of long-term environmental change and short-term geological events in the northeastern Mediterranean region, which forms the basis for improving understanding of the influence of major geological and environmental events on the biological evolution of endemic species.