The level of protection provided by the present environmental risk assessment (ERA) of fungicides in the European Union for fungi is unknown. Therefore, we assessed the structural and functional implications of five fungicides with different modes of action (azoxystrobin, carbendazim, cyprodinil, quinoxyfen, and tebuconazole) individually and in mixture on communities of aquatic hyphomycetes. This is a polyphyletic group of fungi containing key drivers in the breakdown of leaf litter, governing both microbial leaf decomposition and the palatability of leaves for leaf-shredding macroinvertebrates. All fungicides impaired leaf palatability to the leaf-shredder Gammarus fossarum and caused structural changes in fungal communities. In addition, all compounds except for quinoxyfen altered microbial leaf decomposition. Our results suggest that the European Union’s first-tier ERA provides sufficient protection for the tested fungicides, with the exception of tebuconazole and the mixture, while higher-tier ERA does not provide an adequate level of protection for fungicides in general. Therefore, our results show the need to incorporate aquatic fungi as well as their functions into ERA testing schemes to safeguard the integrity of aquatic ecosystems.