Macrophytes play an important role in maintaining biodiversity. However, little is known about the relationships between different types of macrophytes and the diversity of aquatic communities. The purpose of this study was to determine the relationships between floating and submerged macrophytes and the temporal variation in the taxonomic and functional diversity of phytoplankton in two tropical reservoirs (Cursai and Cajueiro) located in Northeastern Brazil. A field study was carried out quarterly between November 2018 and November 2019 to analyze the taxonomic (richness, equitability, and Shannon index) and functional (FRic, FEve, and FDiv) diversity indices of phytoplankton in relation to the presence of macrophytes. Taxonomic and functional diversity indices varied over time in sampling sites. Macrophytes had positive effects on taxonomic richness, Shannon index, and FDiv in Cajueiro, and negative effects on the taxonomic equitability and FEve of phytoplankton in Cursai. Functional diversity of phytoplankton was negatively influenced by water transparency and positively by total dissolved solids, pH, and nitrate in sites with macrophytes, while taxonomic richness was positively influenced by total phosphorus. Our results showed that taxonomic and functional diversity of phytoplankton responded differently to spatial and temporal variation, and species richness, Shannon index and FDiv were related to macrophytes.