Selenium (Se(VI)) is environmentally toxic. One of the most popular reducing agents for Se(VI) remediation is zero-valent iron (ZVI). However, most ZVI studies were carried out in water matrices, and the recovery of reduced Se has not been investigated. A water-sediment system constructed using natural sediment was employed here to study in-situ Se remediation and recovery. A combined effect of ZVI and unacclimated microorganisms from natural sediment was found in Se(VI) removal in the water phase with a removal efficiency of 92.7 ± 1.1% within 7 d when 10mgL-1 Se(VI) was present. Soluble Se(VI) was removed from the water and precipitated to the sediment phase (74.8 ± 0.1%), which was enhanced by the addition of ZVI (83.3 ± 0.3%). The recovery proportion of the immobilized Se was 34.2 ± 0.1% and 92.5 ± 0.2% through wet and dry magnetic separation with 1gL-1 ZVI added, respectively. The 16s rRNA sequencing revealed the variations in the microbial communities in response to ZVI and Se, which the magnetic separation could potentially mitigate in the long term. This study provides a novel technique to achieve in-situ Se remediation and recovery by combining ZVI reduction and magnetic separation. Environmental ImplicationThe toxicity and bioaccumulation of selenium (Se) render it a concerning pollutant; however, its increasing demand necessitates recovery. This study provides novel insights into in-situ Se remediation and recovery by combining ZVI reduction with magnetic separation. We investigated the immobilization process of Se(VI) and its subsequent recovery through dry and wet magnetic separations using natural sediment. Additionally, the potential mitigation of their hazardous ecological effects was explored by examining alterations in the microbial community of the sediment after wet magnetic separation. This work emphasizes that the combination of ZVI and magnetic separation presents a new option for in-situ Se recovery.