The effects of the humic acid (HA) nature and the activated carbon (AC) surface chemistry on the effectiveness of HA removal were investigated. Brown (BHA) and gray (GHA) humic acid fractions of different structure and physicochemical properties were tested in the adsorption process using mesoporous ACs. The modification of chemical structure and surface properties of AC was achieved by ammonization (AC/N) and hydrogen treatment (AC/H). Both approaches led to a decrease in the oxygen content followed by an increase in the carbon basicity, maintaining the porous texture of AC nearly unaltered. Over twice higher removal degree of BHA and GHA was observed for the modified ACs. The kinetics of adsorption of HA fractions have been discussed using the pseudo-second-order model and the intraparticle diffusion model. All ACs showed a higher adsorption capacity toward BHA compared to GHA, which is mainly attributed to the lower molecular weight of BHA. The shape of the equilibrium isotherms indicates a strong competition between water and HA molecules for adsorption sites of the carbon surface.