A wide range of cyanobacterial species and their harmful metabolites are increasingly detected in water bodies worldwide, exacerbated by climate change and human activities. The resulting bloom conditions represent significant challenges to production of safe drinking water and cost effective water reuse, therefore their removal is a priority to ensure public safety. While current microscopic taxonomy identification methods provide valuable information about cell numbers during treatment, these methods are incapable of providing information about the fate of cells during treatment. The objectives of this study were to (1) identify the critical control points for breakthrough and accumulation of cells by investigating the fate of cells during treatment processes using a combination of taxonomy, cell integrity and next-generation sequencing (NGS), and (2) assess the impact of pre-treatment processes on breakthrough prevention at critical control points, and the benefits of cell integrity and NGS analysis for improved management purposes. This paper presents the results of an unprecedented cyanobacterial monitoring program conducted in four full scale water treatment plants located in three different climate zones. Cyanobacterial cell integrity and accumulation during operation process were assessed for the first time using next generation of gene sequencing methods. NGS analysis led to detection of cyanobacterial and melainabacteria orders in water samples that were not identified by microscopy. 80 ± 5% of cells were completely lysed post pre-oxidation (for both ozone and potassium permanganate). However unlike pre-ozonation, the remaining cells were undamaged cells with the potential to accumulate and grow within the plants post-KMnO treatment, particularly in clarifier sludge. To effectively monitor water quality, this study presents a synergistic approach coupling new and traditional analytical methods and demonstrates the importance of identifying critical points for managing accumulation of cyanobacteria within plants.