Freshwater harmful algal blooms (HABs) have been a major challenge for many decades, affecting water supplies, recreational use of water and aquatic ecosystems. The blooms of most concern, and that receive the greatest research attention, are toxic cyanobacteria. Much of the research focus has been on understanding the response of cyanobacterial species and communities to environmental conditions. As cyanobacteria are prokaryotes and have relatively simple genomes, they have been the focus of molecular studies that complement traditional ecological and physiological approaches. These complementary approaches have provided new insights into understanding how cyanobacteria species respond to environmental conditions. Molecular and physiological studies are increasingly focussed on strain variability and the implications for managing and modelling blooms and toxin production. Additionally, there have been substantial advances in techniques used to measure and monitor blooms including remote sensing, pigment sensors and molecular methods. Despite the research which has improved understanding of the physiology of cyanobacteria, and an enhanced ability to measure HABs at the scales needed to link environmental drivers and blooms, there has been a less rapid development of deterministic models. Improved coordination and collaboration amongst disciplines is essential to enhance our ability to predict the timing and extent of harmful cyanobacterial blooms.