Photochemical reactions are major pathways for the removal of Hg species from aquatic ecosystems, lowering the concentration of monomethylmercury (MMHg) and its bioaccumulation in foodwebs. Here, we investigated the rates and environmental drivers of MMHg photodegradation and inorganic Hg (IHg) photoreduction in waters of two high-altitude lakes from the Bolivian Altiplano representing meso- to eutrophic conditions. We incubated three contrasting waters in situ at two depths after adding Hg-enriched isotopic species to derive rate constants. We found that transformations mostly occurred in subsurface waters exposed to UV radiation and were mainly modulated by the dissolved organic matter (DOM) level. In parallel, we incubated the same waters after the addition of low concentrations of natural MMHg and followed the stable isotope composition of the remaining Hg species by compound-specific isotope analysis allowing the determination of enrichment factors and mass-independent fractionation (MIF) slopes (Δ199Hg/Δ201Hg) during in situ MMHg photodegradation in natural waters. We found that MIF enrichment factors potentially range from −11 to −19‰ and average −14.3 ± 0.6‰ (1 SE). The MIF slope diverged depending on the DOM level, ranging from 1.24 ± 0.03 to 1.34 ± 0.02 for the low and high DOM waters, respectively, and matched the MMHg MIF slope recorded in fish from the same lake. Our in situ results thus reveal (i) a relatively similar extent of Hg isotopic fractionation during MMHg photodegradation among contrasted natural waters and compared to previous laboratory experiments and (ii) that the MMHg MIF recorded in fish is characteristic for the MMHg bonding environment. They will enable a better assessment of the extent and conditions conducive to MMHg photodegradation in aquatic ecosystems.