Cyanobacteria thrive in eutrophic freshwaters and impose a serious problem for the management of water bodies. Some Cyanobacteria species impose even a risk for public health due to the production of intracellular toxins. This study is a qualitative approach to determine the degree of toxicity and the toxicological aspect of cyanotoxins in order to setup a monitoring program for cyanobacteria blooms and the management of cyanotoxins thriving in three water bodies in Northern Morocco. Water samples were collected from three major water reservoirs/dams near the city of Tétouan (SMIR, BELMEHDI and NAKHLA). These water samples were screened for possible Cyanobacteria using specific culture media (BG13 & Z8). Three cyanobacteria species (Microcystis aeruginosa, Pseudanabaena galeata and Oscillatoria tenuis) were isolated, purified and lyophilized. Using gas chromatography coupled with mass spectrometry, nine types of microcystins were characterized namely: (MC-LR); (MC-YR); (MC-LA); (MC-FR); (MC-RF), [Mser 7 ]MC-LR; [Dha 7 ]MC-LR; MC-YAba; and [Mser 7]MC-YR. Our results strongly recommend and urge different stakeholders to consider the various health risks potentially generated by these toxins during water use and management. In addition, this study is a contribution to raise awareness of the toxicological aspect of the cyanobacteria inhabiting the water bodies of Northern Morocco.