We developed an anaerobic baffled reactor (ABR) for the energy-saving and efficient anaerobic treatment of nitrogen-containing pollutants in aquaculture wastewater. The ABR was operated with sludge from the secondary sedimentation tank of an urban sewage treatment plant for 150 d. When the total nitrogen load was 0.150 kg/m3·d, 90.20 and 99.83% of NH4+–N and NO2−–N were removed, respectively, and 84.51% of chemical oxygen demand decreased. The activated sludge in the ABR was analyzed to investigate biological properties, including extracellular polymers, specific anaerobic ammonium oxidation activity, cytochrome C, hydrazine dehydrogenase activity, polysaccharide (PS), and extracellular protein (PN). When the activated sludge was treated, the ratio of PN to PS (PN/PS) in extracellular polymers increased 55 times, specific anaerobic ammonium oxidation activity increased 2 times, and hydrazine dehydrogenase activity increased 1.4 times, while cytochrome C concentration decreased. The results revealed that the anaerobic ammonium oxidation activity was significantly improved. The morphology of the activated sludge observed with an electron scanning microscope became appropriate for treating the sludge. Although the microbial species in the sludge were not diverse, the dominant bacterial community was identified, which contributed to the increased granularity.