Sediment contamination by heavy metals has become a widespread problem that can affect the normal behaviors of rivers and lakes. After chitosan/Fe0-nanoparticles (CS-NZVI) beads were cross-linked with glutaraldehyde (GLA), their mechanical strength, stability and separation efficiency from the sediment were obviously improved. Moreover, the average aperture size of GLA-CS-NZVI beads was 20.6 μm and NZVI particles were nearly spherical in shape with a mean diameter of 40.2 nm. In addition, the pH showed an insignificant effect on the removal rates from the sediment. Due to the dissolution of metals species into aqueous solutions as an introduction of the salt, the removal rates of all heavy metals from the sediment were increased with an increase of the salinity. The competitive adsorption of heavy metals between the sediment particles and GLA-CS-NZVI beads became stronger as the sediment particles became smaller, leading to decreased removal rates. Therefore, the removal efficiency could be enhanced by optimizing experimental conditions and choosing appropriate materials for the target contaminants.