Cyanotoxins and taste and odor (T&O) compounds produced by cyanobacteria are some of the main emerging water contaminants. Cyanobacteria are prokaryotic photosynthetic microorganisms present in most ecosystems. Cyanobacteria have long been recognized for their nitrogen-xing capacity, which contributes to global soil and water fertility. The chapter aims to evaluate the influence of global climate change on the presence of freshwater toxins and the associated risks for different water uses. It describes the known factors that influence the proliferation of cyanobacteria and their toxin production and the possible influence of climate change on each of these factors. The chapter discusses the potential risks associated with the proliferation of toxic species for drinking water production and water recreational activities. It demonstrates that eutrophication and increase in water temperature directly influence the frequency and duration of cyanobacterial blooms, as well as that of related issues such as toxins and T&O compounds in freshwater sources.