In the DEEP core from the Lake Ohrid ICDP drilling project, the carbon isotope composition of bulk organic matter (δ 13 CTOC) over the last 516 ka shows a negative correlation with total 2 organic carbon (TOC) and total inorganic carbon (TIC). This relationship is marked by periods of lower δ 13 CTOC values corresponding to higher TIC and TOC. Along with TOC/TN, the correlation between δ 13 CTOC and δ 13 CTIC suggests that most of the organic matter in the core is from aquatic primary production within the lake. The combination of TOC, TIC, and δ 13 CTOC is able to disentangle long-term glacial/interglacial cycles and, to a lesser extent, millennial scale climate variability. Over the longer term, δ 13 CTOC shows modest variability, indicating that the δ 13 C of the dissolved inorganic carbon (DIC) pool is stabilised by the supply of karst spring water characterised by δ 13 CDIC influenced by the bedrock δ 13 C value, and the long residence time of the lake water and well mixed upper water column promoting equilibration with atmospheric CO2. However, comparison between arboreal pollen (AP%), TIC and TOC data indicates that the δ 13 CTOC signal is modulated by the leaching of soil CO2 through runoff and spring discharge, changes in primary productivity, and recycling of organic matter within the lake, all affecting δ 13 CDIC. Exceptionally low δ 13 CTOC during some interglacial periods (e.g. MIS7 and MIS9) possibly indicate rapid intensification of organic matter recycling and/or increasing stratification and enhanced methanogenesis, even if the latter process is not supported by the sedimentological data.