A microcosm system that included river sediment, water and different zeolite capping materials (natural zeolite, surfactant-modified zeolite (SMZ), or aluminum modified zeolite (AMZ)) was designed to study the effect of capping on the release of phosphorus and three organic pollutants (phenol, pyridine, and pyrene) from the sediment to the overlying water over the course of three month. For the same amount of the three capping materials, the efficiency of phosphorus inactivation was in the order of SMZ>AMZ>natural zeolite. The inactivation of phosphorus was mainly caused by the covering effect, co-precipitation and adsorption by the capping materials. The different zeolites gave different results for the release of phenol, pyridine, and pyrene from the sediment. When natural zeolite was used as the capping material, there was no effect on the release of pyrene and pyridine, whereas capping the sediment with SMZ or AMZ inhibited the release of pyrene and pyridine but to different extents. However, for controlling the release of phenol from the sediment, aluminum modified zeolite was the most efficient material, whereas no effects were observed when natural zeolite or SMZ were used. The different capabilities of the zeolite materials for controlling the release of different organic pollutants are related to the differences in the electrical properties of these pollutants.