Seventy-one percent of our planet’s surface consist of water, but only 0.6% are lentic and lotic freshwater habitats. Often taken for granted, freshwaters are immensely diverse habitats and host >10% of all animal and >35% of all vertebrate species worldwide. However, no other major components of global biodiversity are declining as fast and massively as freshwater species and ecosystems. Urbanisation, economic growth, and climate change have increased pressure on freshwater resources, whilst biodiversity has given way to the increasing demands of a growing human population. The adverse impacts on aquatic ecosystems include habitat fragmentation, eutrophication, habitat loss, and invasion of pathogenic as well as toxic species. Although there is increasing evidence that freshwater fungal diversity is high, the study of the biodiversity of freshwater fungi is still in its infancy. In light of the rapid decline in freshwater biodiversity, it is timely and necessary to increase our efforts to evaluate the diversity and potential ecological function of this fascinating and diverse group of freshwater organisms.