The macrophyte–periphyton complex has great importance for the functioning of shallow lakes and reservoirs. Several observations in the field have suggested that macrophyte life-form and architecture seem to be very important for periphytic algal community organization. To test the influence of macrophytes on periphyton, we compared the algal community structure and nutrient status (C, N, P) of periphyton on the stem and leaves of Utricularia foliosa L., and on a nylon thread utilized as an artificial substrate. Furthermore, this study aims to assess the seasonal variation of limnological conditions and their influence on Utricularia-periphyton complex. Spring and summer had higher light conditions, P availability and macrophyte cover than autumn and winter. Algal biomass, total density, and biovolume were higher on natural substrate than on artificial. Algal assemblages changed with season and species descriptors differed among substrates types. Phosphorus content of periphyton was generally more correlated with water nutrient availability than with N and C content. Periphyton on free-floating submersed macrophytes may have great importance on the functioning of shallow tropical reservoirs, particularly in the clear water state. Moreover, seasonal variation of limnological conditions determines the periphyton-Utricularia relationships and either intensifies or minimizes the macrophyte influence on periphyton.