Pollen and δ13CTOM data obtained from two contrasting lake sequences (Lakes Kamalété and Nguène), located 200 km apart in the lowland rainforest of Gabon, provide complementary local and regional 1500-yr records of high resolution (15–30 yr) vegetation change. A combination of aquatic, semi-aquatic and terrestrial pollen showed in both records that the tropical rainforest increased during periods of high rainfall and decreased during drought intervals. The strong fluctuations of water balance at decadal scale during the “Medieval Warm Period” (not, vert, similar 1100–800 cal yr BP) coincided with a noticeable increase in shade-intolerant taxa, indicating recurring rainforest canopy disturbance. The δ13CTOM signal showed high-amplitude variations in both records, which positively correlates with the rainforest dynamics and local vegetation changes. The similar trends in both the pollen and the δ13CTOM signals between these sites demonstrate the regional broadly synchronous timing of shifting hydrological conditions. The largely positive co-variation between strong fluctuations of hydrological conditions and changes in rainforest structure and composition indicate that regional climatic change is probably the driving force for major rainforest dynamics in Gabon. Any significant anthropogenic impact on vegetation has not been clearly identified, and this issue still needs to be resolved independently by obtaining detailed archeological records across the interval 1400–800 BP, which currently seem to be extremely rare or not easily available.