The toxic potential of mercury (Hg) in aquatic systems is due to the presence and production of methylmercury (MeHg). Recent studies in tropical floodplain environments showed that periphyton associated with the roots of aquatic macrophytes produce MeHg. Periphyton communities are the first link in the food chain and one of the main MeHg sources in aquatic environments. The aim of this work was to test the hypotheses that the algal community structure affects potential methylation, and ecologically distinct communities with different algal and bacterial densities directly affect the formation of MeHg in the roots of macrophytes. To evaluate these, net MeHg production in the roots of Eichhornia crassipes in relation to the taxonomic structure of associated periphytic algae was evaluated. Macrophyte root samples were collected in the dry and flood season from two floodplain lakes in the Pantanal (Brazil). These lakes have different ecological conditions as a function of their lateral hydrological connectivity with the Paraguay River that is different during times of drought. Results indicated that MeHg production was higher in the flood season than in the dry season. MeHg production rates were higher in the disconnected lake in comparison to the connected lake during the dry season. MeHg production exhibited a strong positive co-variation with cyanobacteria abundance (R(2)=0.78; p<0.0001 in dry; R(2)=0.40; p=0.029 in flood) and with total algal biomass (R(2)=0.86; p<0.0001), and a negative co-variation with Zygnemaphyceae (R(2)=0.50; p=0.0018) in the lake community in dry season. This indicates that ecological conditions that favour the establishment and development of cyanobacteria are associated with higher rates of methylation in aquatic systems. This suggests that cyanobacteria could be a proxy for sites of MeHg production in some natural aquatic environments.