Freshwater fungi are a diverse group of organisms and fulfill important functions in the food web dynamics of surface water ecosystems. Ascomycetic and basidiomycetic hyphomycetes play key roles in leaf litter breakdown in rivers and creeks, while parasitic chytrids are an important food source for small invertebrates in lakes. Field studies indicate that fungal communities are affected by fungicides at environmentally relevant concentrations. However, despite their ecological importance, freshwater fungi are currently not specifically addressed in the EU regulatory frameworks with respect to the protection of surface waters. Specifically, the prospective risk assessment of fungicides does not evaluate adverse effects on non-target aquatic fungi. This paper aims to describe important functions of freshwater fungi, provides an overview of adverse effect levels of fungicides on this organism group, and proposes to integrate the fungal community of freshwater ecosystems as an additional trophic level in the current fungicide risk assessment frameworks. Results of a literature review on the effects of fungicides on aquatic fungi revealed that information on the toxicity of fungicides to non-target aquatic fungi is limited. This is, in part, due to the lack of standardized bioassays using aquatic fungi as test species. Although there is an encouraging number of bioassays focusing on the degradation of dead organic material by hyphomycetes, studies on fungicide effects on other important ecological functions, like the control of algal blooms in lentic surface waters by parasitic chytrid fungi, or on mutualistic fungi living in the guts of aquatic arthropods are largely missing. Thus, the further development and standardized of different fungi bioassays is recommended.