Aquatic pathogenic fungi play a pivotal role in aquatic ecosystems due to their diversity, abundance and impacts on the other organisms and the ecosystem. Taxonomic surveys suggest a vast, largely undiscovered fungal diversity. Various well-documented examples of disease-inducing species exist within the Ascomycota, Oomycetes, Chytridiomycetes and other fungal-like organisms, with impacts upon diverse hosts, including algae, fish, amphibians, reptiles, crustaceans, molluscs and corals. The non-photosynthetic nature of fungi underscores their ecological roles as saprophytes or parasites, often with intricate interactions among fungal species and their hosts. Aquatic pathogenic fungi are crucial components of aquatic environments, including in aquacultural systems, adapting their life cycles to overcome challenges presented by water-based ecosystems. Life cycles involve multiple stages of development that, regardless of variation, have an acute ability to disperse in water and locate their hosts. The ability to produce spores plays a vital role in the dispersal, survival and infection capabilities of these fungi. Environmental factors strongly influence the prevalence and virulence of these fungi by directly or indirectly affecting their growth, reproduction and pathogenicity in aquatic ecosystems. These factors, varying with fungal species, aquatic ecosystems and host demographics, are significantly impacted by human activities like aquaculture, habitat alteration, water pollution and introduction of non-native species, which can create conducive environments for fungal proliferation or disrupt natural ecosystems, thereby contributing to disease outbreaks.