Currently the demand for antibiotic free aquaculture has increased, but to which extend AMR spreads in aquaculture in the absence of antibiotic additives remains to be elucidated. Therefore, we aimed to reveal potential factors that affect AMR in antibiotic free aquaculture systems. As a model system, we utilized enclosed recirculating aquaculture containing African catfish (Clarias gariepinus). We sampled water and biofilms during various rearing periods and performed 16S ribosomal RNA (rRNA) high-throughput sequencing and qPCR for six antibiotic resistance genes (ARGs), the class 1 integron integrase gene intI1 and the 16S rRNA gene. In parallel, we monitored the physicochemical water parameters during the duration of aquaculture application. During the rearing operation nitrogen compounds accumulated to 42.00 ± 18.17 mg/L ammonium, 153.0 ± 7.5 mg/L nitrate and 2.9 ± 0.9 mg/L nitrite. However, this did not influence the dominant bacterial communities or ARG abundance in either biofilm or aquatic samples. Despite the absence of antibiotic use, ARGs consistently occurred in high relative abundance, but at constant levels (e.g. sul1: −2.0 ± 1.5 log10 copies/16S rRNA) during rearing. Moreover, one ARG, the β-lactamase gene blaTEM was significantly associated with the bacterial biofilm lifestyle. Its abundance further correlated with the taxonomic composition and α-diversity of the microbial communities. In conclusion, ARGs, were present in high relative abundance, but remained stable during the period of recirculating aquaculture. Consequently, bacterial communities were able to retain high ARG abundance during aquaculture operations, despite the absence of selective pressures.