Halloysite particles, with their unique multilayer nanostructure, are demonstrated here as highly efficient and readily available sorbent of heavy metals that can be easily scaled up and used in large-scale water remediation facilities. The various methods of raw material purification were applied, and their effects were verified using techniques such as BET isotherm (determination of specific surface area and size of pores), XRF analysis (composition), and SEM imaging (determination of morphology). A series of adsorption experiments for aqueous solutions of metal ions (i.e., lead, cadmium) were carried out to quantify the sorption capacity of halloysite particles for selected heavy metals. The ability of adequately activated halloysite to efficiently remove heavy metal ions from water solutions was confirmed. The value of the zeta potential of raw and purified halloysite particles in water was determined. This enables us to understand its importance for the sorption of positively charged ions (metal, organics) at various pH values. The adsorption process conducted in the pH range of 6.0–6.5 showed significant improvement compared to the acidic conditions (pH value 3.0–3.5) and resulted in a high sorption capacity of lead ions—above 24.3 mg/g for the sulphuric acid-treated sample. The atomic scale ab initio calculations revealed a significant difference in adsorption energy between the external siloxane surface and cross-sectional interlayer surface, resulting in pronounced adsorption anisotropy. A low energy barrier was calculated for the interlayer migration of heavy metals into the halloysite interior, facilitating access to the active sites in these regions, thus significantly increasing the sorption capacity and kinetics. DFT (density functional theory) calculations supporting this study allowed for predicting the sorption potential of pure halloysite structure towards heavy metals. To confront it with experimental results, it was crucial to determine proper purification conditions to obtain such a developed structure from the mineral ore. The results show a massive increase in the BET area and confirm a high sorption potential of modified halloysite towards heavy metals.