Lake Oubeira, a shallow Mediterranean lake located in El-Kala National Park, northeastern Algeria, has faced frequent cyanobacterial blooms during the summer and autumn seasons, primarily due to human activities. While prior studies have investigated cyanobacteria abundance and toxin levels in the lake's fauna, they have not identified the specific genera responsible for toxin production or the environmental factors influencing their fluctuations. This study, conducted between 2016 and 2017, involved sampling the lake at one-meter depth across four seasons and identified 23 genera from five orders, with nine genera accounting for 93.68% of total abundance. The most prevalent genera included Microcystis (44.51%), Planktothrix (16.27%), Pseudanabaena (8.38%), Aphanocapsa (6.06%), Synechococcus (3.73%), Cylindrospermum (3.98%), Cylindrospermopsis (3.93%), Dolichospermum (3.17%) and Aphanizomenon (3.65%). Seasonal variations in distribution and abundance were noted, with significant blooms primarily composed of Microcystis and Planktothrix occurring during summer and autumn, coinciding with peak microcystin concentrations. The highest levels recorded were in the summer (9.57μg MC-LR equivalent. L-1) and autumn (10.09μg MC-LR equivalent. L-1). Strong positive correlations were observed between microcystin levels, chlorophyll-a concentration, and the abundance of Microcystis and Planktothrix. Microcystin was detected in all samples, with the lowest concentration (1.31μg MC-LR equivalent. L-1) found in spring. The presence of potentially toxic cyanobacterial genera was consistent throughout the year, regardless of seasonal or weather changes. To mitigate risks for lake users, continuous monitoring is essential to identify and quantify cyanobacteria and their toxins, particularly focusing on seasonal variations in this shallow lake ecosystem.