Aquatic fungi are usually microscopic organisms, which do not produce visible fruiting bodies but grow asexually as well as sexually. Their occurrence in water is rather subtle and specialised methods are needed to examine their diversity, population structure and ecological function. Aquatic fungi, being heterotrophs, are reliant upon photosynthetically produced organic matter. In the case of small particles such as algae, pollen, seeds and zooplankton carcasses, decomposition is achieved by the much smaller Oömycetes and Chytridiomycetes, rather than the aquatic Hyphomyctes. These fungi cause severe damage to larger aquatic organisms mainly fishes or fish eggs. This is of great importance for aquaculture since it necessitates antifungal treatments, but even in natural systems, watermoulds have the potential to severely harm the indigenous fish population. It has been shown that food web manipulations greatly alter the fungal biomass in lakes which suggests that saprophytic fungi transfer organic matter directly to the higher trophic levels of aquatic food webs. This distinctly indicates that watermoulds constitute an integral part of the aquatic ecosystem and aquatic food web.