In the present study, we explore a new application of Barite (BaSO4) as a sequestering phase for selenite (Se(IV)) and selenate (Se(VI)) ions from aqueous solutions because of the low solubility and high stability of Barite with its ability to selectively incorporate a large amount of various ions. The uptake of Se(IV) and Se(VI) during coprecipitation with Barite was investigated through batch experiments to understand the factors controlling effective removal of Se(IV) and Se(VI) from polluted water to Barite. The factors include (i) chemical affinity related to the degree of surface complexation between Barite surface and Se(IV)/Se(VI) ion and (ii) structural similarity related to the structural geometry of incorporated ions into the substituted site. The uptake of Se(IV) by Barite is dependent on pH, coexistent calcium ion, and sulfate concentration in the initial solution, possibly due to their effects on the chemical affinity and structural similarity. On the other hand, the uptake of Se(VI) by Barite was strongly dependent on sulfate concentration in the initial solution, which is only related to the structural similarity. This study describes the mechanisms for Se distribution between Barite and water, thereby providing a good estimate of its ability to effectively remove Se(IV) and Se(VI) from aqueous solutions under optimized experimental parameters examined here.