Biological filter (biofilter) technology has developed rapidly and has been extensively employed to remove nitrogen pollutants originating from aquatic environments. Due to the different responses of nitrogen microorganisms to various operating parameters and environmental factors, achieving satisfactory nitrogen removal in biofilters remains a challenge. Hence, this review aims to provide useful information on the underlying nitrogen removal mechanisms in biofilters by giving a comprehensive review of traditional and newly discovered nitrogen transformation processes and microbial communities associated with nitrogen cycling. Firstly, a brief summary on overall performance of biofilters using traditional and newly discovered methods for nitrogen removal was presented. The detailed nitrogen transformation pathways and functional microbial communities associated with nitrogen cycling in biofilters were discussed. A brief overview is followed by a more detailed discussion of techniques for assessing nitrogen microbial population dynamics and community structure and function. Finally, conclusions and recommendations for future work are highlighted.