Aquatic macrophytes are affected by spatial and temporal scales, which may drive their successful establishment and development. Environmental variations can determine the distribution and composition of plants due to habitat requirement of each species. The presence of certain species or life forms in the aquatic environment can help in prediction of abiotic changes. In this study, we aimed to relate physicochemical aspects of water with community structure of aquatic macrophytes during one hydrologic cycle, in three lakes of Parque Estadual do Rio Doce, the newest Ramsar Site in Brazil. Fixed plots were marked on the shoreline of these lakes. Vegetation cover of macrophytes was assessed bimonthly in the field together with some physicochemical variables. The relationship between vegetation cover and abiotic data was confirmed by principal coordinate analysis. In general, species and life forms of macrophytes were sensitive to the physicochemical variables dissolved oxygen, pH and transparency, that significantly affected the distribution of plant cover. Thus, we suggest the use of the abiotic variables described in our study plus topographic profile of the shoreline to evaluated macrophyte distribution in other lakes.