The effects of climate change on long-term mercury (Hg) cycling are still not well understood, as climate changes are usually gradual and can only be assessed using high-resolution archives. Our study site (a small, lowland tectonic lake in Sulawesi, Indonesia) provides a unique opportunity to further understanding of Hg cycling in the Southeast Asian (SEA) tropics during the transition from the Pleistocene to the Holocene, a period of significant climate variability. We present a high-resolution record of Late Glacial and Holocene Hg deposition within the sediments of tropical Lake Lantoa, Sulawesi. Using a multi-proxy framework (including pollen, charcoal, carbon:nitrogen ratio and high-resolution geochemistry records) we investigate the response of Hg accumulation rates (HgAR) in sediments to shifts in climate between ∼16,488 and 538 cal BP. This period encompasses the Bølling-Allerød (BA) warming, Younger Dryas (YD) cooling and Holocene warming events, providing new insights into the effects of global climatic transitions on HgAR in SEA sediments. The Pleistocene Termination had the highest HgAR and substantial variability (µ = 11.32, 5.38–33.91 μg m−2 yr−1), when drier conditions and high charcoal accumulation rates suggest that fire activity was the main source of Hg to the lake. The Holocene Transition was marked by a decrease in HgAR (µ = 8, 3.50–18.84 μg m−2 yr−1) as humid conditions precluded forest burning, followed by high HgAR (µ = 11.35, 3.30–158.32 μg m−2 yr−1) in the Early Holocene. Mercury accumulation rate in the Late Holocene (µ = 3.80, 1,67–43.65 μg m−2 yr−1) was the lowest in the Lake Lantoa record, marked by the lowest fire events and a stable catchment. An increase in carbon:nitrogen ratios during the Late Holocene, coupled with a decrease in HgAR, suggests that the establishment of lowland forest resulted in suppressed Hg erosion/leaching. Our results demonstrate that forest fires, vegetation change and volcanism are important drivers of Hg inputs to Lake Lantoa, a relationship which is strongly mediated by climate and lake-catchment dynamics.