The progressive build-up of toxic wastes, such as ammonia and heavy metals, is a problem of intensive fish culture systems. . This study was conducted to determine the effects of the natural zeolite (clinoptiolite) in removing ammonia and heavy metals. Twelve cement ponds (each 2m³) were used to carry out three experimental zeolite treatments with the following concentrations: 1kg/1000L, 2kg/1000L, and 3kg /1000L (with three replications, in addition to 0 concentration for the control. The clinoptilolite was placed in mesh bags (25x20 cm). Twenty mono-sex male Nile tilapia, O. niloticus, fingerlings, with an average initial weight of 21.10, 20.43, 22.70 and 22.40g for control, T1, T2 and T3, respectively, were stocked in each tank. The results revealed that application of zeolite significantly (P<0.05) decreased all the inorganic dissolved nitrogen. The average concentrations of unionized ammonia (NH₃) were 0.52, 0.39, 0.21 and 0.04 mg/l for Control, T1, T2, and T3 during the whole experimental period, whereas the concentrations of nitrate (NO₃-N) were 1.31, 0.91 0.88 and 0.61 mg/l, respectively. The concentrations of nitrite (NO₂-N) were 0.36, 0.31, 0,19 and 0.11 mg/l during the whole experimentation. Zeolite had the ability to take up heavy metals; Cd, Cu, Fe, Mn, Pb and Zn. Heavy metals concentration values in ponds' water showed significant differences (P<0.05) for the control as well as the three treatments, where control ponds had the highest total mean concentrations of all metals (5.771 mg/l,) compared to T1 (4.827 mg/l), T2 (4.083 mg/l) and T3 (3.562mg/l), respectively. Heavy metals accumulation in musculature of O. niloticus in different treatments was investigated. All metals showed significant (P<0.05) differences among different treatments.