The El Guájaro reservoir, situated in northern Colombia, holds significant economic and ecological importance. It is categorized as eutrophic due to factors such as wastewater discharges, agricultural practices, and the dragging of limestone material. These factors create favorable conditions for cyanobacterial proliferation. This study evaluates the diversity and abundance of cyanobacteria, with special attention to the genera identified as toxin producers, and bloom formers within the reservoir. Sampling was conducted in the photic zone at seven stations during both rainy and dry seasons between 2015 and 2019. Abundance and diversity were quantified using the iNEXT program, while a beta diversity analysis assessed community differentiation in relation to environmental parameters. A total of 86 species from 12 orders and 42 genera were identified, with 44% of these species noted as potentially toxic. A significant predominance of filamentous species was identified. Pseudanabaena and Phormidium were the most frequent and abundant genera. The results reveal distinct distribution and abundance patterns influenced by seasonal fluctuations. A notable bloom, co-dominated by Microcystis and Dolichospermum, occurred during the 2019 dry season, leading to the mortality of livestock and other animals. Urgent governance measures and control strategies are imperative to mitigate the health impact of such blooms.