The expansion of harmful cyanobacterial blooms is of worldwide concern as they have increased globally in frequency and intensity in recent decades. A cyanobacterial colony was found in a bottle of natural mineral water of a small water company in July 2012, which led to a further examination for a period of five months (July-November 2012) of both the bottled filtered water and the originating groundwater source (N. Greece) for the occurrence of Cyanobacteria. Cyanobacteria occurrence was monitored by microscopy and cyanospecific 16S rDNA amplification; potentially toxic species occurrence was screened by mcyA gene (known to take part in the MC-biosynthetic gene cluster) amplification. The highest abundance of cyanobacterial cells without the simultaneous presence of the mcyA gene, was measured in July, in contrast to October when the presence of cyanobacteria was only identified by tracing cyanospecific 16S rDNA and the mcyA gene region in the underground water source. The results of this small scale monitoring program indicate the potential existence of an emerging danger for human health in a relatively manageable product such as the bottled natural mineral water.