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Global biodiversity decline is believed to be caused by high anthropopressure. Particularly vulnerable habitats are freshwater ecosystems, which are hotspots of biodiversity. The threat to these ecosystems are cyanobacterial blooms, which tend to proliferate in the face of climate changes. Cyanobacteria development and dominance affect the whole food web, especially the zooplankton community. We used three classical biodiversity indexes (species richness, Simpson's Diversity Index and Shannon Diversity Index) and three functional diversity indexes (functional richness, functional evenness and functional divergence) to study the impact of cyanobacterial bloom on the zooplankton community. The study was conducted in water bodies with a different period of bloom duration (short-lasting blooms vs. long-lasting blooms) in order to determine the impact of the proliferated blooms on the aquatic ecosystems. Use of functional diversity indexes allowed for identifying changes that can be overlooked by classical biodiversity indexes. We conclude that cyanobacterial bloom involves modifications of functional trait space of studied communities and, in consequence, functioning of aquatic ecosystems.