A nearshore core (LT03-05) from the north basin of Lake Tanganyika provides diatom, pollen, and sedimentary time series covering the last ca. 3800 yr at 15–36 yr resolution. A chronology supported by 21 AMS dates on terrestrial and lacustrine materials allows us to account for ancient carbon effects on 14C ages and to propose refinements of the region's climatic history. Conditions drier than those of today were followed after ca. 3.30 ka by an overall wetting trend. Several century-scale climate variations were superimposed upon that trend, with exceptionally rainy conditions occurring 1.70–1.40 ka, 1.15–0.90 ka, 0.70–0.55 ka, and 0.35–0.20 ka. Around 0.55–0.35 ka, during the Spörer sunspot minimum, drier conditions developed in the northern Tanganyika basin while more humid conditions were registered at Lakes Victoria and Naivasha. This indicates significant variability in the nature and distribution of near-equatorial rainfall anomalies during much of the Little Ice Age.