Dissimilatory Fe(III) reduction has a profound infl uence on the global cycling of elements and the decontamination of pollutants, depending on the interaction of various environmental conditions. Hydrogelencapsulated goethite/soil was prepared in this study, and anaerobic incubation was conducted to investigate the biological Fe reduction of different encapsulated aggregates by Shewanella oneidensis MR-1. Results indicated that the release of Fe(II) ion was signifi cant and insignifi cant in R-soil treatments with and without anthraquinone-2,6-disulfonate (AQDS), respectively. The increase in the cross-linker ratio in the hydrogel decreased iron reduction. The Fe(II) concentration followed the order of unencapsulated treatment < 0.3% encapsulated hydrogel treatment < 2% encapsulated hydrogel treatment with AQDS addition. The results of the goethite experiment suggested that the goethite level and the addition of AQDS changed the effect of mineral structure property on iron reduction. This result was consistent with the simulation of a reductive dissolution kinetic model, in which the initial iron reduction rate k and long-term Fe(II) ion release extent parameter log γ were controlled by the interaction of the mineral structure property, iron mineral content, and electron shuttle compound distribution. Thus, site-specific environmental conditions should be fully considered in monitoring the performance and environmental effects of biological iron reduction.