Andean Patagonian lakes are oligotrophic systems characterized by low dissolved organic carbon (DOC) levels and moderate to high Hg concentration that determine naturally high Hg/DOC ratios and bioavailability. In these lakes, microbial food webs are extremely important in Hg trophodynamics, being that the picophytoplankton fraction is a major entrance path of Hg²⁺ into pelagic food webs. This study analyzed the bioaccumulation of Hg²⁺ by the picocyanobacteria Synechococcus sp. using the radiotracer ¹⁹⁷Hg²⁺ and water from four Andean Patagonian lakes presenting a natural gradient of DOM concentration and quality. Hg²⁺ bioaccumulation by Synechococcus was calculated as the uptake of Hg²⁺ per biovolume unit (volume concentration factor VCF; pL μm⁻³). Hg uptake showed a wide variation (13 < VCF< 300 pL μm⁻³) in the natural DOC gradient tested (0.7–4 mg L⁻¹; Hg²⁺/DOC ratio; 1.8–14 ng mg⁻¹). The bioaccumulation of Hg²⁺in Synechococcus decreased exponentially with DOC concentration. Differences in the quality of dissolved organic matter (DOM) among lake water influenced also Hg²⁺ bioaccumulation. Naturally degraded DOM, with low molecular weight/size, promoted higher Hg uptakes in Synechococcus compared to humic DOM, rich in high molecular weight/size aromatic compounds, that retained Hg in the dissolved phase. In Andean Patagonian lakes picocyanobacteria are pivotal organisms in the Hg cycling, taking dissolved Hg²⁺ and transferring it to pelagic food webs, as well as fueling the benthic Hg pathway through sedimentation.