The increasing levels of industrial wastewater released to the environment present a serious threat to human health, living resources, and ecological systems. Fe-modified zeolites were developed and tested for removal of Cu2+ and Zn2+ from contaminated water. The surfaces of the naturally occurring zeolite, clinoptilolite, were modified with Fe(III) oxyhydroxides using three different methods, denoted I, II, and III (FeCli1, FeCli2, and FeNaCli1, respectively). The oxyhydroxides were prepared in Method I using 0.1 M FeCl3·6H2O in an acetate buffer (pH = 3.6); in Method II, using 10% FeCl3·6H2O solution in 0.1 M KOH (pH = 10); and Method III was the same as Method I except the clinoptilolite was pretreated with NaCl. Newly synthesized materials from these three methods were then tested for their ability to enhance the sorption capacity for Cu and Zn compared to the natural sample (Cli). Powder X-ray diffraction measurements and the chemical composition of these modified samples confirmed that clinoptilolite maintained its structure while amorphous Fe3+ species were synthesized. The specific surface area (BET method) of both the natural and modified clinoptilolite increased by 2 and 7.5 times for Methods I and II, respectively. Scanning electron microscopy and energy dispersive X-ray spectroscopy revealed that CaO was formed during Method I (FeCli1). Throughout the adsorption process, the hydrolysis of CaO and the release of OH− caused the precipitation of Cu and Zn hydroxide, which made the determination of the sorption capacity of FeCli1 impossible. This phenomenon was avoided in Method III (FeNaCli1) because of the absence of exchangeable Ca2+. The adsorption experiments with Method II resulted in double-enchanced adsoprtion capacity. Laboratory batch experiments revealed that the sorption capacities increased in the following order: Cli < FeCli2 < FeNaCli1, for Cu: 0.121 mmol/g < 0.251 mmol/g < 0.403 mmol/g and for Zn: 0.128 mmol/g < 0.234 mmol/g < 0.381 mmol/g.