Cyanobacteria often have a deleterious effect on zooplankton. We hypothesized that the presence of either M. aeruginosa cells or microcystin extracts from M. aeruginosa would have a significant impact on the population growth rate, survivorship, and fecundity of Moina cf. micrura isolated from L’Albufera, Valencia, Spain. The cladocerans were exposed to different concentrations of Microcystis extracts on a diet of Nannochloris oculata (Chlorococcales) as well as different proportions of Microcystis single cells and N. oculata. Cyanotoxins were extracted from a Microcystis bloom by its repeated freezing, thawing, and sonication. Total microcystin concentration was 138.2 µg l−1. M. aeruginosa single cells were obtained by sonication. We used five microcystin concentrations (from 4.3 to 69.1 µg l−1 and controls without microcystins) with non-toxic Nannochloris oculata at 0.5 × 106 cells ml−1 as diet or on different proportions of M. aeruginosa single cells and N. oculata. Microcystin reduced generation time and longevity of M. cf. micrura but increased daily production of offspring. Single-celled Microcystis (100%) diet for Moina cf. micrura decreased growth rates compared with treatments using cyanotoxin extracts. We suggest routine testing of cyanobacterial crude extracts using plankton to estimate harmful impacts of blooms especially for drinking water reservoirs.