Cyanobacteria can form intense and sometimes toxic blooms in all kinds of aquatic ecosystems, typified as cyanobacterial bloom. Cyanobacterial blooms can create a range of harmful toxins, which may disturb water sources, successively posing serious health threat to living organisms, and at this stage they are termed as cyanobacterial harmful algal blooms (CyanoHABs). The occurrence of cyanobacterial blooms and cyanobacterial toxins are globally reported, so is the evident in Bangladesh, mainly trigged by increased anthropogenic eutrophication and global climate change.Cyanobacterial blooms and the accumulation of several toxins in human's drinking water, recreational water and aquatic biota such as zooplankton, fish larvae and juveniles interrupt aquaculture, aquatic ecosystem and public health in Bangladesh. As the management measures of toxic cyanobacteria and cyanotoxin are insufficient in Bangladesh, and the proper management for mitigating the worldwide occurrence of toxic cyanobacterial blooms is crucial for maintenance and sustainable development of functional ecosystems, some recommendations are illustrated. Further appropriate research on biology and ecology of cyanobacteria, cyanobacterial toxins and their relationship with environmental factors as well as nutrient management in fish ponds to manage noxious and harmful algae is essential to minimize their adverse impacts on aquaculture and public health for the country.