Investigating mercury (Hg) interactions with phytoplankton is crucial for understanding Hg cycling in aquatic ecosystems and informing management practices. Anthropogenic activities have increased bioavailable Hg, impacting human and environmental health. Phytoplankton, at the base of the food chain, facilitate Hg entry and transformation, making their study essential for Hg risk mitigation. Field and lab analyses reveal that pico-microplankton from Lake Geneva and Lake Greifen differ in Hg accumulation and transformation based on eutrophication levels and water chemistry. Diatom Cyclotella meneghiniana was found to bioaccumulate Hg species and alter Hg speciation (namely in MeHg demethylation and Hg(II) reduction), with distinct metabolic changes in response to Hg(II) and MeHg exposure. Additionally, different algae species demonstrated Hg(0) uptake and oxidation capacities, with green algae exhibiting higher Hg(0) uptake. These findings highlight the complex role of phytoplankton in Hg cycling and emphasize the importance of species-specific responses to Hg pollution in aquatic environments.