Structural characteristics of algal communities can be used to access environmental conditions, but there is a great need to identify the drivers of change in all habitats. This study evaluated the spatial and temporal changes in the phytoplankton, epipelon and epiphyton structures in a shallow reservoir. We investigated the determining factors of the structural variability and spatial differences in the species composition and algal density in the three habitats. Bimonthly samplings were carried out for determination of the limnological variables and algal communities. The rainy season was characterized by high nutrient availability and macrophyte coverage, and the communities were dominated by flagellate algae, as Chromulina elegans Doflein. The highest modification rate was found in the phytoplankton structure, followed by epiphyton and epipelon. Despite the species co-occurrence among phytoplankton, epipelon and epiphyton, the descriptor species presented different representativeness in communities. Planktonic and epiphytic algae were more associated with temporal variation in nutrient availability, while depth was more important for epipelic algae structuring. We conclude that the algal community in the plankton, epipelon and epiphyton was structured by different environmental factors, but descriptor species co-occurrence suggested an interrelationship between communities in this shallow reservoir with high abundance of macrophytes.