The dataset comprises marine sediment core KC-13 from Central Aegean, Greece (38°14',6012; 25°06',2470, 652 m water depth), spanning from ~ 42,500 years BP to the present. The gravity core was retrieved during the OTE-2019 (HCMR, RV Aegaeo, 2019). The dataset includes radiocarbon ages, high-resolution grain-size and X-ray fluorescence (XRF) core scanning data, strontium (Sr) and neodymium (Nd) isotope data of terrigenous sediment fraction and stable carbon (δ13C) isotope records from planktonic foraminifera (Globigerina bulloides). These data provide insights into terrigenous sediment provenance, transport pathways and hydrographic variability in the Aegean Sea from the late glacial to the Holocene.