Charismatic megafauna species may act as both flagship and umbrella species. They influence local environments and biotas, determine related ecosystem processes and functions, and are associated with high levels of biodiversity. However, the intrinsic characteristics of megafauna species including long lifespan, large body size, sparseness and/or rarity, late maturity, and low fecundity, as well as high market value, make them very prone to extinction. Up to now, scientific interest and conservation efforts have mainly focused on terrestrial and marine megafauna, while freshwater species have received comparatively little attention, despite evidence suggesting that freshwaters are losing species faster than marine or terrestrial realms. The high susceptibility of freshwater megafauna to multiple threats, coupled with immense human pressure on freshwater ecosystems, places freshwater megafauna amongst the most threatened species globally. The main threats include overexploitation, dam construction, habitat degradation, pollution, and species invasion. These threats increase mortality, decrease productivity, and reduce fitness, causing the decline of populations and the extinction of freshwater megafauna species. Given the essential ecological and biological roles of freshwater megafauna, further research should focus on their distribution patterns, extinction risks, and population dynamics, thereby improving the knowledge base for conservation planning. Finally, freshwater megafauna‐based conservation strategies may raise public awareness for freshwater conservation and therefore benefit a broader range of freshwater species and functions. WIREs Water 2017, 4:e1208. doi: 10.1002/wat2.1208 This article is categorized under: Water and Life > Conservation, Management, and Awareness Water and Life > Nature of Freshwater Ecosystems Water and Life > Stresses and Pressures on Ecosystems Freshwater megafauna are facing a wide range of threats that could lead to the decline of populations, reduction of genetic variability, and species extinction.