The use of ecotoxicological techniques for the evaluation of the quality of limnetic waters allows the early detection of toxic agents that pose risks to human health. In this study Moina micrura (two clones), Daphnia laevis (two clones) and Daphnia similis, a temperate species, were used to evaluate the toxicity of six Microcystis extracts from two Colombian reservoirs. Toxin was detected and quantified by HPLC. Microcystin-LR was found in all extracts with the highest concentrations in one sample from each reservoir (434 μg g(-1) and 538 μg g(-1)). The extracts that had the highest toxin concentration also had the highest toxicities to cladocerans. Measurement of 48-h LC50 showed consistent differences between cladoceran species but not clones, Also, reproduction data in two species were consistent with the MC-LR content of one sample tested, with decreased reproduction and disruption of egg production. However, only some growth results of neonates exposed to extracts were consistent with the acute response. In conclusion, Daphnia species are a good model for monitoring cyanotoxins as they respond in a sensitive way to natural phytoplankton samples containing microcystin-LR.