© 2017 Informa UK Limited, trading as Taylor & Francis Group. This study proposes a biological nitrogen removal system for freshwater aquaria consisting of a down-flow hanging sponge (DHS) and an up-flow sludge blanket (USB). DHS–USB systems can perform nitrification and denitrification simultaneously, reducing ammonia (NH3) and nitrate (NO3−) toxicity in the water. The performance of the system was evaluated using on-site fresh water aquaria at ambient temperature (23–34°C) over 192 days. NH3 and nitrite (NO2−) were maintained at a detection limit of 0.01 mg N L−1 and NO3− was maintained below 10 mg N L−1, despite limited water exchange. The 16S rRNA gene of microorganisms from the sludge retained in the bioreactors was sequenced to identify the microbial communities present. Microbial community analysis revealed that ammonia oxidizing archaea (AOA), Ca. Nitrososphaera and Nitrosopumilus, played an important role in nitrification in the DHS reactor, while denitrifying bacteria Thauera played an important role in denitrification in the USB reactor. The proposed DHS–USB system is a promising technological advancement in the development of lower maintenance aquaria.