The Tibetan Plateau (TP), known as the “Third Pole”, is a critical zone for atmospheric mercury (Hg) deposition. Increasing anthropogenic activities in the globe leads to environmental changes, which may affect the loading, transport and deposition of Hg in the environment. However, the deposition history and geochemical cycling of Hg in the TP is still uncertain. Our records of Hg and Hg isotopes in sediment profiles of the two largest lakes in the TP, Lake Qinghai and Nam Co, show increased Hg influx since last century, with the maximum Hg influx enrichment ratios of 5.4 and 3.5 in Lake Qinghai and Nam Co, respectively. Shifts in negative δ ²⁰²Hg in Lake Qinghai (−4.55 to −3.15‰) and Nam Co (−5.04 to −2.16‰) indicate increased atmospheric Hg deposition through rainfall, vegetation and runoff of soils. Mass independent fractionation of both even-Hg (∆ ²⁰⁰Hg: +0.05 to +0.10‰) and odd-Hg (∆ ¹⁹⁹Hg: +0.12 to +0.31‰) isotopes were observed. Positive Δ ²⁰⁰Hg suggest high proportion of precipitation-derived Hg in the TP, whereas the positive Δ ¹⁹⁹Hg results from Hg(II) photo-reduction. Both lakes show increasing Δ ¹⁹⁹Hg since the 1900 s, and we conclude that with the decrease of ice duration, Hg(II) photo-reduction may have been accelerated in these TP lakes.