AbstractThe impact of sodium dodecyl sulfate (SDS, as model linear anionic surfactant) dosage on overall nitrogen removal performance of anammox reactor alongside its microbial population and sludge properties was investigated. In this study (day 136), an anmmox sequencing batch biofilm reactor was subjected to gradual dosage of SDS from 0 to 20 mg L−1. Intriguingly, results revealed that SDS at ≥7.5 mg L−1 prompted sludge disintegration, evidenced by increased protein and polysaccharide content in the effluent. Nevertheless, reactor's average total nitrogen removal efficiency slightly improved from 83.12% (0 mg L−1) to 86.3% (20 mg L−1). The 16S rRNA gene sequencing revealed that SDS dosing significantly suppressed the unwanted and unavoidable nitrite oxidizing bacteria (NOBs) in the reactor as the abundance of genus Nitrospira declined from 40.68% (day 1) to 19.15% (day 136). The abundance of anammox genus Candidatus Kuenenia significantly improved from 1.86% (day 1) to 40.02% (day 136) as a result of NOB suppression. This study revealed that low concentration of surfactants in wastewater does not affect the anammox bacteria in a biofilm reactor. Furthermore, adding low concentrations of SDS (≥7.5 to 20 mg L−1) to wastewater may effectively suppress notorious NOBs in biofilm‐based anammox systems.