The desmids constitute a highly diverse group with potential as a bioindicator of the conservation status of freshwater environments. We evaluated the changes in the desmid community on macrophytes with different structural complexities within mixed stands in a floodplain shallow lake in the Brazilian semi-arid region. Our main question was whether the environmental variables that best predict desmid structure among macrophyte species in mixed stands. Samplings were performed at each two months at four fixed stations during one year in a shallow tropical lake. To assess the changes in community structure, we sampled the periphyton on three macrophytes species (Cabomba caroliniana, Nymphaea amazonum, and Utricularia foliosa) with different complexity levels, which were quantified by their fractal dimension. Multivariate analysis showed that the structure and composition of the periphytic desmids were influenced by fractal dimension, nutrient availability, and temperature. The richness, density, and diversity of desmids differed between macrophytes with complex structure (U. foliosa and C. caroliniana) and simple structure (N. amazonum). We also observed that more complex macrophytes have a greatest contribution of desmids with small cell (< 40 mu m) in the community, suggesting that the substrate complexity affects the use of habitat. Our results suggest that the substantial fractal differences between host macrophytes are a major determining factor in the structure of periphytic desmid communities.