Harmful cyanobacterial efflorescence is of growing global concern and its prediction and management require a better understanding of the growth control factors and dominance of cyanobacteria. The Zit-Emba reservoir located in the North-East of Algeria, was constructed to provide drinking water, irrigation, and fishing. The vertical and seasonal distribution variation of cyanobacteria community associated with environmental factors was comprehensively investigated from April 2016 to December 2016 at five depths, based on a seasonal sampling. The cyanobacteria communities of this reservoir are composed of seven genera belonging to five orders. The average proportion of Microcystis to total cyanobacteria population was 43%, followed by Woronichinia 21%, Planktothrix 16%, Dolichospermum 13%, Oscillatoria 5%, and the remainder (Merismopedia, Spirulina) 2%. The average cyanobacterial abundance was 2702 cells/mL, ranging from 360 to 65 795 cells/mL and this abundance exceeds the alert level 1 throughout the year. The most recurrent periods of increase took place from spring to summer and autumn. However, the vertical distributions of cyanobacteria displayed a similar profile each season, and abundances tended to decrease with depth. The results of the statistical analysis suggested that the most abundant of cyanobacterial genera were positively related to chlorophyll-a and water temperature and negatively with the concentrations of NO3-N, NH4-N, and NO2-N. This demonstration of toxigenic cyanobacteria in this drinking water production dam involves regular monitoring of the cyanobacterial communities and cyanotoxins in raw water.