The purpose of this study was to produce novel eco-friendly organoclays for removing toxic elements from aqueous environment. In the present research, nano-bentonite (Bent) and nano-montmorillonite (MT) minerals were treated with novel ionic liquids including 1-methyl-3-octylimidazolium chloride ([Omim][Cl]), 3,3′-(hexane-1,6-diyl) bis (1-methyl-imidazolium) bromide chloride ([H(mim)2[Br][Cl]), and 1-hexyl-3-methylimidazolium chloride ([Hmim][Cl]) to produce organoclays with ecofriendly features. The products were investigated using X-ray diffraction (XRD); Fourier transformed infrared spectroscopy (FTIR); carbon, hydrogen, and nitrogen elemental analysis (CHN); scanning electron microscope (SEM); and specific surface area (SSA) (via N2-BET method) techniques. Finally, the mechanism involved in the adsorption of Pb(II) and Hg(II) onto organoclays from the aqueous phase was investigated by applying most three popular experimental adsorption isotherms including Langmuir, Freundlich, and Sips models. The results showed that by intercalating ILs, first XRD diffraction (d001) of the modified clays was increased. Based on the results of Sips model, [H(mim)2]-clays and [Omim]-clays had maximum adsorption capacity and maximum adsorption affinity. To the best of the authors’ knowledge, the amount of removed toxic metals by the modified clays in this research was more than those in the previous researches. This research demonstrated that clay mineral modifications using ILs is enhanced clay d-spacing and facilitated diffusion of the large hazardous metal ions into clay interlayer spaces. These increased their potential for toxic metal immobilization as green adsorbents.