Inert media such as plastic, ceramic or zeolite are conventionally used for wastewater biofiltration. They all need microbial activation and are essentially chosen for their surface/mass ratio, since biofiltration is entirely performed within the surface biofilm. Using biodegradable media may enhance the sustainability of the system, but it should not produce decomposition-related pollutants. Due to their surface extension, peculiar microbiota and structural resistance, aquatic moss appears to be a very good support for biofilters. Thus, in this study, we evaluated aquatic moss mats as an alternative medium for biofiltration of aquaculture or aquaponic effluents. Two moss species, Taxiphyllum barbieri and Leptodictyum riparium, were tested, also for their contribution on nitrogen metabolism and potential negative effects on hydroponic plants cultivation, due to competition for nutrients. Our proof-of-concept research demonstrates equivalence in real conditions, as inert and moss media exhibited comparable rates; however, the amount of moss required can be several times lower than that of any competing media. Preliminary results suggest the possibility to integrate moss-based biofilters in aquaculture and aquaponics technologies.