The Lesser Flamingo is an endangered bird species, and the local population numbers and distribution fluctuate considerably in its main habitat — the East African Rift Valley lakes. These fluctuations are caused by unexplained decreases in the abundance of its main food source, Arthrospira fusiformis, which is a fast-growing, alkaliphilic cyanobacterium. Samples collected from Lake Nakura now reveal that cyanophage infection is responsible for sudden breakdowns of A. fusiformis biomass. The study reports cyanophage concentrations of up to 7 × 109 per ml, which are some of the highest values that have ever been reported in the environment, and A. fusiformis infection rates reached up to 25% of the total bacterial population. During the study, flamingo numbers at Lake Nakuru decreased from more than one million to 1,500, which highlights the importance of phage predation for this bottom-up trophic cascade.