The presence of microcystins (MCs) in waters exclusively intended for drinking water production is a major problem for both ecosystems and public health.  The current study aimed to identify the environmental factors that explain the spatial and temporal variations in the abundance of cyanobacteria and the concentration of microcystins in the Guenitra Dam, a Mediterranean water body used for drinking water production, irrigation supplies, and fisheries. The Guenitra Dam waters are mesotrophic to eutrophic; they shelter nine genera of cyanobacteria in which Microcystis flosaquae is dominant in the frequency of occurrence and densities. Cyanobacterial densities in the Guenitra Dam exceed the level of vigilance in January; alert level 1 was shown during the rest of the year and alert level 2 was in November, with a peak registration of more than 189 million cells / mL. The highest cell densities were found in surface waters and decreased with depth. In autumn, more than 99% of the overall cyanobacteria density was detected. The MC-LR contents did not exceed 0.5 µg.L-1 except in November (1.02 µg.L-1 in St5) and December (1.5 µg.L-1 in St4). From January to September, the levels did not surpass 0.22 µg.L-1. Statistical analysis revealed the existence of very highly significant (p <0.0001) positive correlation of M. flosaquae with microcystins (MC-LR) and highly significant (p <0.001) of M. flosaquae with NH₄⁺. During the bloom found in November, the presence of MC-LR in the drinking water was recorded, with a concentration of 0.57 µg.L-1, which is clearly higher than that allowed (0.1 µg.L-1) by the WHO. The presence of MC-LR in the drinking water is indicative of a failure in the water treatment process. The presence of cyanobacteria and cyanotoxins in raw and drinking waters of the Guenitra reservoir involves regular monitoring of the cyanobacterial communities and cyanotoxins in raw water.