The Marano and Grado Lagoon is well known for being contaminated by mercury (Hg) from the Idrija mine (Slovenia) and the decommissioned chlor-alkali plant of Torviscosa (Italy). Experimental activities were conducted in a local fish farm to understand Hg cycling at the sediment–water interface. Both diffusive and benthic fluxes were estimated in terms of chemical and physical features. Mercury concentration in sediments (up to 6.81μg/g) showed a slight variability with depth, whereas the highest methylmercury (MeHg) values (up to 10ng/g) were detected in the first centimetres. MeHg seems to be produced and stored in the 2–3cm below the sediment–water interface, where sulphate reducing bacteria activity occurs and hypoxic–anoxic conditions become persistent for days. DMeHg in porewaters varied seasonally (from 0.1 and 17% of dissolved Hg (DHg)) with the highest concentrations in summer. DHg diffusive effluxes higher (up to 444ng/m2/day) than those reported in the open lagoon (~95ng/m2/day), whereas DMeHg showed influxes in the fish farm (up to −156ng/m2/day). The diurnal DHg and DMeHg benthic fluxes were found to be higher than the highest summer values previously reported for the natural lagoon environment. Bottom sediments, especially in anoxic conditions, seem to be a significant source of MeHg in the water column where it eventually accumulates. However, net fluxes considering the daily trend of DHg and DMeHg, indicated possible DMeHg degradation processes. Enhancing water dynamics in the fish farm could mitigate environmental conditions suitable for Hg methylation.