Cyanobacterial blooms have become a frequent phenomenon in freshwaters worldwide; they are a widely known indicator of eutrophication and water quality deterioration. Information and knowledge contributing towards the evaluation of the ecological status of freshwaters, particularly since many are used for recreation, drinking water, and aquaculture, is valuable. This Special Issue, entitled “Advancing Knowledge on Cyanobacterial Blooms in Freshwaters”, includes 11 research papers that will focus on the use of complementary approaches, from the most recently developed molecular-based methods to more classical approaches and experimental and mathematical modelling regarding the factors (abiotic and/or biotic) that control the diversity of not only the key bloom-forming cyanobacterial species, but also their interactions with other biota, either in freshwater systems or their adjacent habitats, and their role in preventing and/or promoting cyanobacterial growth and toxin production.