The eutrophic character of a growing number of freshwaters around the world is a global health concern as in these high nutrient ecosystems toxic cyanobacteria often bloom. The well-studied cyanobacterial toxins are microcystins (MCs), a family of more than 90 closely related hepatotoxic heptapeptides. Since MCs are products of the first trophic level, they tend to accumulate in the food chain. Moreover, there is evidence suggesting that irrigation with contaminated water results in severely contaminated crops. As expected, scientific efforts have focused on the elucidation of mechanisms for cyanobacterial bloom formation and toxicity in these eutrophic freshwaters. However, recent studies indicated that oligotrophic freshwaters are also prone to toxic cyanobacterial blooms. In this context, we compared the toxic potential of two low nutrient lakes in NW Greece to a eutrophic lake of the same region. Interestingly, in seston samples, MC concentrations were found to be higher in these lakes. Cyanobacterial communities were compared based on molecular data. Our findings suggest that the MC producers are mainly cosmopolitan non-diazotrophic cyanobacteria. In conclusion, based on the results, monitoring programs should be established for oligotrophic lakes to prevent of health hazards from use of such "innocent" ecosystems.