While mercury (Hg) is a major concern in all aquatic environments because of its methylation and biomagnification pathways, very few studies consider Hg cycling in remote alpine lakes which are sensitive ecosystems. Nineteen high-altitude pristine lakes from Western/Central Pyrenees were investigated on both northern (France) and southern (Spain) slopes (1620–2600 m asl.). Subsurface water samples were collected in June 2017/2018/2019 and October 2017/2018 for Hg speciation analysis of inorganic mercury (iHg(II)), monomethylmercury (MMHg), and dissolved gaseous mercury (DGM) to investigate spatial and seasonal variations. In June 2018/2019 and October 2018, more comprehensive studies were performed in four lakes by taking water column depth profiles. Besides, in-situ incubation experiments using isotopically enriched Hg species (199iHg(II), 201MMHg) were conducted to investigate Hg transformation mechanisms in the water column. While iHg(II) (0.08–1.10 ng L−1 in filtered samples; 0.11–1.19 ng L−1 in unfiltered samples) did not show significant seasonal variations in the subsurface water samples, MMHg (<0.03–0.035 ng L−1 in filtered samples; <0.03–0.062 ng L−1 in unfiltered samples) was significantly higher in October 2018, mainly because of in-situ methylation. DGM (0.02–0.68 ng L−1) varies strongly and can exhibit higher levels in comparison with other pristine areas. Depth profiles and incubation experiments highlighted the importance of in-situ biotic methylation triggered by anoxic conditions in bottom waters. In-situ incubations confirm that significant methylation, demethylation and photoreduction extents are taking place in the water columns. Overall, drastic environmental changes occurring daily and seasonally in alpine lakes are providing conditions that can both promote Hg methylation (stratified anoxic waters) and MMHg photodemethylation (intense UV light). In addition, light induced photoreduction is a major pathway controlling significant gaseous Hg evasion. Global warming and potential eutrophication may thus have direct implications on Hg turnover and MMHg burden in those remote ecosystems.