This study aimed at analyzing the structure of epiphytic algal community on aquatic macrophytes morphologically different and in distinct hydrological periods at a lentic environment (Pombas Lake) located in the Upper Parana River floodplain. In this study we tested the hypothesis that epiphyton richness, diversity, density, and composition, associated with submerged macrophytes are affected by hydrological dynamics and by habitat heterogeneity. The macrophytes used as substrates were Eichhornia azurea Kunth, an emergent macrophyte, and Egeria najas Planch, a submerged macrophyte. The samplings were performed quarterly in 2009, the species richness, diversity, density, and composition of the epiphytic algal community were evaluated. The species richness was not different between the substrates. Regardless of the evaluated substrate, the month of March had the highest species richness and diversity, especially of Desmids and Chlorophyceae. E. najas recorded the greater variation in abundance, compared with E. azurea. Bacillariophyceae, independent of the period and substrate, represented over 50 % of total density. The species composition was different among the periods, in which March and June (low water) were more similar and formed the group I, while September and December (high water) formed the group II. In summary, the hypothesis was accepted, since we verified that the hydrological dynamics of the floodplain is the direct controlling factor on structure of epiphytic algal community, and the substrate heterogeneity is the indirect controlling factor.