The datasets include measurements of mercury, total organic, and inorganic carbon in sediment samples from core BOS04-5B, extracted from Lake Bosumtwi in 2004 as part of the ICDP Lake Bosumtwi Drilling Project. Lake Bosumtwi is the only natural lake in Ghana, western Africa (6°300 N, 1°250 W), and occupies a meteorite impact crater dated to 1.08 ± 0.04 Ma: one of the youngest and best-preserved impact craters on Earth. Focusing on the uppermost ∼ 47 m of the BOS04-5B sediment record, this data was generated to assesses whether major shifts in local hydroclimate produced measurable changes in how Hg has been transported to, and buried within, this system since ∼ 96 ka. Total Hg (HgT) in the bulk sediments of the core was measured using an RA-915 portable mercury analyser with a PYRO-915+ pyrolyser, Lumex, at the University of Oxford (UK). For this study, we analysed 165 samples spanning the composite depth interval 47.7 to 0 m, with an average temporal resolution of ∼ 0.6 ka between each sample (range: 0.01 to 5.85 kyr). Quantitative values for total organic carbon (TOC) and total inorganic carbon (TIC) content were measured on the same powdered sample material also analysed for Hg, using a Stroehlein Coulomat 702 at the University of Oxford (UK). Analytical reproducibility for this instrument was ≤ 0.2% based on repeat measurements, with a detection limit of ca. 0.1 %-0.2 %.