Cyanobacterial (blue-green algal) blooms are one of the common consequences of the increasing eutrophication of surface waters. The production of cyanobacterial toxins and their presence in drinking and recreational waters represents a growing danger to human and animal health. Due to a lack of toxin standards and to resource limitations on the wide-scale use of analytical methods (e.g., high-performance liquid chromatography, enzyme-linked immunosorbent assay (ELISA)) in cyanobacterial toxin monitoring, it is necessary to assess and to develop additional methods for their detection and estimation. Microbiotests using invertebrates offer a possible approach for the inexpensive and straightforward detection and assessment of cyanobacterial bloom toxicity. Three microbiotests with: Thamnocephalus platyurus, Daphnia magna, and Spirostomum ambiguum were examined with bloom samples containing hepatotoxic microcystin-LR and up to five additional microcystin variants. Two kinds of cyanobacterial bloom sample preparations were tested: crude extracts (CE) and purified extracts (PE). The highest toxicity was found when CE was used for microbiotests. The sensitivity of microorganisms decreased from S. ambiguum to T. platyurus and to D. magna. A statistically significant correlation was found between microcystin concentration and T. platyurus biotest, and between mouse bioassay and S. ambiguum results. Addition of Me2SO (1%, v/v) is a possible method to increase the sensitivity of the microorganisms for microcystin-LR.