Harmful algal blooms are among the emerging threats to freshwater biodiversity that need to be studied further in the Anthropocene. Here, we studied freshwater plankton communities in ten tropical reservoirs to record the impact of algal blooms, comprising different phytoplankton taxa, on water quality, plankton biodiversity, and ecosystem functioning. We compared water quality parameters (water transparency, mixing depth, pH, electrical conductivity, dissolved inorganic nitrogen, total dissolved phosphorus, total phosphorus, chlorophyll-a, and trophic state), plankton structure (composition and biomass), biodiversity (species richness, diversity, and evenness), and ecosystem functioning (phytoplankton:phosphorus and zooplankton:phytoplankton ratios as a metric of resource use efficiency) through univariate and multivariate analysis of variance, and generalized additive mixed models in five different bloom categories. Most of the bloom events were composed of Cyanobacteria, followed by Dinophyta and Chlorophyta. Mixed blooms were composed of Cyanobacteria plus Bacillariophyta, Chlorophyta, and/or Dinophyta, while non-bloom communities presented phytoplankton biomass below the threshold for bloom development (10 mg L−1, WHO alert level 2). Higher phytoplankton biomasses were recorded during Cyanobacteria blooms (15.87–273.82 mg L−1) followed by Dinophyta blooms (18.86–196.41 mg L−1). An intense deterioration of water quality, including higher pH, eutrophication, stratification, and lower water transparency, was verified during Cyanobacteria and mixed blooms, while Chlorophyta and Dinophyta blooms presented lower pH, eutrophication, stratification, and higher water transparency. All bloom categories significantly impacted phytoplankton and zooplankton structure, changing the composition and dominance patterns. Bloom intensity positively influenced phytoplankton resource use efficiency (R2 = 0.25; p < 0.001), while decreased zooplankton resource acquisition (R2 = 0.51; p < 0.001). Moreover, Cyanobacteria and Chlorophyta blooms negatively impacted zooplankton species richness, while Dinophyta blooms decreased phytoplankton richness. In general, Cyanobacteria blooms presented low water quality and major threats to plankton biodiversity, and ecosystem functioning. Moreover, we demonstrated that biodiversity losses decrease ecosystem functioning, with cascading effects on plankton dynamics.
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