Aluminum and iron oxides have been often used in the coagulation processes during water purification due to their unique surface properties toward anions. In the presence of silica, the coprecipitation of Al/Si or Fe/Si might decrease the efficiency of wastewater purification and reuse. In this study, surface properties and molecular structures of Al/Si and Fe/Si coprecipitates were characterized using spectroscopic techniques. Also, the selenite removal efficiency of Al/Si and Fe/Si coprecipitates in relation to their surface and structural properties was investigated. While dissolved silicate increased with increasing pH from Fe/Si coprecipitates, less than 7% of silicate was discernible from Al/Si samples over the range from acidic to alkaline conditions. Our spectroscopic results showed that the associations between Al and Si were relatively stronger than that between Fe and Si in coprecipitates. In Al/Si coprecipitates, core-shell structures were developed with AlO6/AlO4 domains as the shells and Si frameworks polymerized from the SiO2 as the cores. However, Si framework remained relatively unchanged upon coprecipitation with Fe hydroxides in Fe/Si samples. The Si core with Al shell structure of Al/Si coprecipitates shielded the negative charges from SiO2 and thereby resulted in a higher adsorption capacity of selenite than Fe/Si coprecipitates.