Macrophytes can be crucial for maintaining clear water conditions in temperate shallow lakes. However, their restorative potential and role in regulating phytoplankton remains uncertain in tropical lakes. We investigated the effects of emergent (Ludwigia adscendens and Persicaria barbata) and submerged (Vallisneria spiralis) macrophytes on the phytoplankton community of a turbid tropical reservoir. Through two in situ mesocosm experiments (~ 1000 l capacity) lasting 4 weeks, we (1) determined the effects of macrophyte density on phytoplankton biomass and composition, and (2) compared these effects between emergent and submerged macrophytes. In Experiment 1, macrophyte treatments reduced phytoplankton biomass and increased water clarity in a density-dependent manner. Only the ‘high density’ treatment (300 g/m2 emergent and 650 g/m2 submerged macrophytes) induced a taxonomic and functional shift from an initial community dominated by turbid water-adapted filamentous cyanobacteria to one dominated by clear water-adapted green algae and cryptophytes. In Experiment 2, emergent and submerged macrophytes reduced phytoplankton biomass and distinctly altered taxonomic and functional composition, with submerged macrophytes inhibiting Microcystis and stimulating cryptophyte taxa. Our results indicate that macrophytes can induce substantial phytoplankton community shifts in turbid tropical lakes, demonstrating the potential to assist in the reversal from turbid to clear water states during restoration efforts.