This dataset presents total nitrogen (TN) and total sulphur contents (TS) inferred from Lake Ohrid core (North Macedonia, Albania) ICDP5045-1 (DEEP). The dataset supplements previously published geochemical data between 447.12 m depth and the sediment surface from the same core (doi:10.1594/PANGAEA.896848). TN and TS was measured at 16 cm resolution. Core ICDP5045-1 was recovered from 243 m water depths in the central part of the Lake. The sediments of core ICDP5045-1 mainly compose of of hemipelagic, fine-grained deposits with varying organic and inorganic carbon contents. Several tephra layers and infrequent, thin (< 5 cm) mass wasting deposits are intercalated occasionally. The basal age of the sequence of ~1.3 million years at 447.12 m marks the onset of permanent water conditions at Lake Ohrid.