The removal of harmful cyanobacteria has recently become an important target in water management strategies. Various methods have been developed to eliminate these microorganisms including: (1) biological methods, especially with floating treatment wetlands and riparian vegetation; (2) physical methods with aeration, mechanical circulation, and hypolimnetic oxygenation; (3) chemical methods with coagulation and flocculation processes; (4) barley straw. We propose that the in situ mechanical-based micro-sieving process provides an opportunity for this to succeed in practice. The appropriate, selective technical parameters and techniques can result in successful water quality improvement, which is essential to meet Water Framework Directive goals and especially for public health. Additionally, micro-sieving used for removing