Cyanobacterial blooms are increasingly common in aquatic environments worldwide. These microorganisms cause concern due to their ability to produce cyanotoxins. Aquatic organisms, especially zooplankton, are exposed to cyanobacterial toxins by different routes, depending on the bloom phase. During cyanobacterial dominance, zooplankton is exposed to cyanotoxins through the ingestion of cyanobacterial cells, while at the bloom senescence, dissolved toxins are the most representative route. In this study, we assessed the effects of a microcystin-producing strain of Microcystis aeruginosa (NPLJ-4) on clones of the tropical small cladocerans Macrothrix spinosa (two clones) and Ceriodaphnia cornuta (one clone) exposed to intact cells and aqueous cell crude extracts. Short-term toxicity assays and life-table experiments were performed to assess the effects of the toxic M. aeruginosa on the survival and life history of the cladocerans. In the short-term toxicity assay, we found that cladocerans were more affected by intact cells. Both clones of M. spinosa were more affected when exposed to intact cells, while C. cornuta displayed about 5-fold more resistance. On the other hand, crude extracts had a low impact on cladocerans' survival. Also, we observed a significant decrease in survival, fecundity, and growth of animals exposed to sublethal and environmentally relevant concentrations of M. aeruginosa cellular biomass. However, even at high concentrations of dissolved microcystins, the crude extract did not have significant effects on the life history parameters of the cladocerans. Although they can be found during cyanobacterial bloom events, small-bodied cladocerans are still affected by toxic Cyanobacteria depending on the exposure route.