The adsorption of copper on the 2:1 clay mineral illite (0.4 to 20μm in size) was studied using a combination of extended X-ray adsorption fine structure (EXAFS) and hybrid-Density Functional Theory (DFT) modelling. The study evaluates the effect of varying pH and copper concentration on the mechanisms of copper adsorption in solutions at background electrolyte concentration typical of natural surface continental freshwaters in granitic environments. The EXAFS spectra revealed both the elongated square pyramidal and Jahn-Teller octahedral coordinated copper clusters as feasible with the former providing better fits using spertiniite (crystalline copper hydroxide) as model compound. Additionally, ab initio calculations also predicted the square pyramidal geometry to be more stable. Copper ions have four Oeq at an average distance of 1.95(1)Å and two independent Oax at average distances of 2.32(16)Å and 3.06(9)Å, with the latter decreasing to 2.97(2)Å as copper concentration and pH are increased. This may reveal different mechanism by which copper adsorbs on illite, as a weakly bound complex at low pH likely at exchange and edge sites and changing towards more strongly bound complexes at high affinity edge sites at higher pH and copper loads. Above 1% Cu model fits suggest formation of copper oligomers with average Cu-Cu distance of 3.10(2)Å. These occur at pH>6, where the correlation between Cu-Cu and Al-Al distances in the illite edge surfaces supports the formation of surface precipitates.