To help ban the use of general toxic algicides, research efforts are now directed towards the discovery of compounds that are specifically acting as cyanocides. Here, we review the past and look forward into the future, where the less desirable general algicides like copper sulphate, diuron or endothall may become replaced by compounds that show better specificity for cyanobacteria and are biodegradable or transform into non-toxic products after application. For a range of products, we review the activity, the mode of action, effectiveness, durability, toxicity towards non-target species, plus costs involved, and discuss the experience with and prospects for small water volume interventions up to the mitigation of entire lakes; we arrive at recommendations for a series of natural products and extracted organic compounds or derived synthetic homologues with promising cyanocidal properties, and briefly mention emerging nanoparticle applications. Finally, we detail on the recently introduced application of hydrogen peroxide for the selective killing of cyanobacteria in freshwater lakes.