© 2019 Elsevier B.V. To achieve water reuse in recirculating aquaculture systems, intermittent nitrification and denitrification processes using internal fibrous media was proposed. A pre-acclimated Biocord biofilter, with an initial nitrification rate of 17.1 ± 12.4 mg total ammonia nitrogen-N/m2/d was applied in a marine whiteleg shrimp (Litopenaeus vannamei) culture tank. Throughout the experiment, the aerobic nitrification activity of the biofilter was sufficient to control the ammonia and nitrite levels below 0.2 mg-N/L with an accumulation of nitrate up to 50 mg-N/L. The remaining nitrate was successfully removed after shrimp harvest with the same biofilter through anoxic denitrification in conjunction with a methanol supplement at a chemical oxygen demand: nitrate-N ratio of 5:1. With complete nitrogen removal, the water was re-aerated and the next crop of shrimp culture was initiated. In this study, a two-crop shrimp cultivation was performed in sequence in the same tank without water exchange. The microbial diversity was monitored using high-throughput sequencing on Illumina MiSeq, which demonstrated that Proteobacteria (45.3 %), Chloroflexi (18.4 %), and Bacteroidetes (17.1 %) were the most abundant phyla. With an emphasis on nitrogen removal, the family Nitrosomonadaceae and Nitrospiraceae were the dominant nitrifying bacteria during the aerobic nitrification, while a high relative abundance of the Methylophaga and Methylotenera genera was observed under the anoxic condition.