This study presents the surface modification of carbon nanotubes (CNTs) to investigate their efficacy as adsorbents for the removal of mercury (Hg(II)) from aqueous solutions. Thiol groups were conjugated to the open ends of CNTs using a series of carboxylation, reduction, chlorination, and thiolation reactions. The functionalization of carbon nanotubes (CNTs) was validated by Fourier Transform Infrared (FT-IR) Spectroscopy, Transmission Electron Microscopy (TEM), and Scanning Electron Microscopy (SEM). The capacity of surface modified CNTs to remove Hg (II) was investigated in relation to many factors, including adsorbent dose, contact duration, pH, and system temperature. Thiol-functionalized CNTs exhibited superior adsorption of Hg (II) ions relative to carboxylic-functionalized CNTs. The computed values of thermodynamic parameters, including enthalpy change (∆Ho) and entropy change (∆So), were found to be positive, indicating that the adsorption of mercury ions on the surface of CNTs is an endothermic process. The adsorption capacity of all adsorbents was examined using equilibrium isotherms, namely Langmuir and Freundlich, revealing that the highest adsorption capacity was recorded for thiol-functionalized single-walled carbon nanotubes, followed by thiol-functionalized multiwalled carbon nanotubes.