In the in-situ remediation of ammonium (NH4+) in groundwater by a sequential reactive barrier filled with zeolite, it is of great importance to understand the mechanisms of NH4+ sorption to zeolite. In this study, the effect of dissolved natural organic matter on NH4+ sorption to natural Chinese clinoptilolite was studied by batch experiments taking humic acid (HA) as a model substance. The surface of clinoptilolite was characterized by scanning electronic microscopy (SEM). A needle cluster of sorbed HA could be observed on the surface of the clinoptilolite. The negative effect of HA on NH4+ sorption is thought to be their competition for sorption sites, the surface coverage and blockage of the pores of clinoptilolite by HA. The fitting results of kinetic sorption data indicated that the rate-controlling step for NH4+ sorption by clinoptilolite in both NH4+ and NH4+ + HA systems is the heterogeneous chemisorption. The existence of HA (10 mg/L) significantly reduced the initial sorption rate of NH4+, but the effect of a further concentration increase of HA was slight. The effect of HA on maximum sorption capacity was found to be insignificant in the experiments. A high aqueous Ca2+ concentration can decrease the negative effect of HA on NH4+ sorption by precipitation of calcium humate.