Recent Lake Tanganyika Hg deposition records were derived using ¹⁴C and excess ²¹⁰Pb geochronometers in sediment cores collected from two contrasting depositional environments: the Kalya Platform, located mid-lake and more removed from watershed impacts, and the Nyasanga/Kahama River delta region, located close to the lake’s shoreline north of Kigoma. At the Kalya Platform area, pre-industrial Hg concentrations are 23 ± 0.2 ng/g, increasing to 74 ng/g in modern surface sediment, and the Hg accumulation rate has increased from 1.0 to 7.2 μg/m²/a from pre-industrial to present, which overall represents a 6-fold increase in Hg concentration and accumulation. At the Nyasanga/Kahama delta region, pre-industrial Hg concentrations are 20 ± 3 ng/g, increasing to 46 ng/g in surface sediment. Mercury accumulation rate has increased from 30 to 70 μg/m²/a at this site, representing a 2–3-fold increase in Hg concentration and accumulation. There is a lack of correlation between charcoal abundance and Hg accumulation rate in the sediment cores, demonstrating that local biomass burning has little relationship with the observed Hg concentration or Hg accumulation rates. Examined using a sediment focusing-corrected mass accumulation rate approach, the cores have similar anthropogenic atmospheric Hg deposition profiles, suggesting that after accounting for background sediment concentrations the source of accumulating Hg is predominantly atmospheric in origin. In summary, the data document an increase of Hg flux to the Lake Tanganyika ecosystem that is consistent with increasing watershed sediment delivery with background-level Hg contamination, and regional as well as global increases in atmospheric Hg deposition.