Resumo. Abstract Aim To evaluate the structure and dynamics of functional phytoplankton groups (FGs) over a macrophyte cover gradient and their relations with environmental variable in small, shallow clear-water lake. Methods Physical, chemical and phytoplankton analyses were made between August 2014 and June 2015 at three points on the Santa Lucia lake (Paraiba, Brazil). Tukey and Wilcoxon tests were applied to the data followed by CCA and Anova. Results The submerged macrophyte cover and phytoplankton biomass presented high spatial and temporal uniformity. The increase in rainfall induced small variations in functional groups, promoting increase the N group and reduction of the SN. Conclusion The homogeneity in the composition and structure functional groups along macrophyte cover confirm the tendency that in small and shallow lakes communities of limnetic and shoreline zones tend to be similar.