Functional classifications are important for studies with phytoplankton, because they are based on ecological or morphological characteristics. We tested the interference of the macrophyte coverage in taxonomic and functional structure of phytoplankton community. Twelve small reservoirs were visited in September 2015 and May 2016 in semiarid regions of Brazilian northeast. Water samples were collected and abiotic variables were measured using a probe. Macrophyte coverage was recorded using the dot method. The microalgae were classified using taxonomic classification (taxa), morphological functional classification (MBFG) and functional groups (FG). We found 242 taxa, 22 FG and the seven MBFG. Phytoplankton presented an average biomass of 3.8 mg L −1 and a richness average of 38 species in dry period, while during the rainy season the biomass value was 6.2 mg L −1 and the richness, 33 species. The macrophytes had the highest average cover during the rainy season (63%) than the dry season (32%). Spearman analyses showed no correlation between total macrophyte coverage and biomass and richness (taxonomic and functional) of phytoplankton (P > 0.05). However, the growth form of emergent and free-floating macrophytes were selected as explanatory variables in the CCA model performed with the MBFG classification. This model presented greatest explanatory power (57%) when compared to FG classification (21%) and taxonomy (20%). Considering our results, using the MBFG classification is recommended for studies with similar sampling design, because it presents greater explanatory power and expresses the relationship between phytoplankton and aquatic macrophytes.