The contamination of soil and water bodies with mercury from anthropogenic sources such as mining and industry activities causes negative effect for living organisms due to the process of bioaccumulation and biomagnification through the food chain. Therefore, the need for remediation of contaminated areas is extremely necessary and very desirable when it is cost-effective by using low-cost sorbents. This paper compares the sorption abilities of natural and iron-modified zeolite towards Hg(II) ions from aqueous solutions. The influence of pH, solid/liquid ratio (S/L), contact time, and initial concentration on the sorption efficiency onto both zeolites was investigated. At the optimal pH = 2 and S/L = 10, the maximum amount of sorbed Hg(II) is 0.28 mmol/g on the natural zeolite and 0.54 mmol/g on the iron-modified zeolite. It was found that rate-controlling step in mass transfer is intraparticle diffusion accompanied by film diffusion. Ion exchange as a main mechanism, accompanied with surface complexation and co-precipitation were included in the Hg(II) sorption onto both zeolite samples. This is confirmed by the determination of the amount of sorbed Hg(II) and the amount of released exchangeable cations from the zeolite structure as well as by the scanning electron microscopy (SEM) and energy dispersive X-ray analysis (EDS) of saturated zeolite samples. In a wide pH range, 4.01 ≤ pH ≤ 11.08, the leaching of Hg(II) was observed in the amount of only 0.28−0.78% from natural zeolite and 0.07−0.51% from iron-modified zeolite indicating that both zeolites could be used for remediation purposes while the results suggest that modification significantly improves the sorption properties of zeolite.