This study investigates the structural and sorption characteristics of nanostructured polysaccharide biopolymers isolated from the tubers of dahlias (Dahlia spp.) and Jerusalem artichokes (Helianthus tuberosus). The plant raw materials were subjected to preparation and extraction to isolate pectin biopolymers, after which the resulting pectins were purified and dried to a stable state, ensuring their suitability for further physicochemical and sorption studies. The obtained pectin matrices were characterized using scanning electron microscopy (SEM) to analyze morphology and nanostructure, infrared (FTIR) and Raman spectroscopy to identify functional groups, as well as atomic absorption spectrometry to study sorption properties. The use of Raman spectroscopy further confirmed the presence of characteristic structural fragments of pectin and revealed changes in the vibrational spectra of functional groups upon interaction with metal ions. The ability of biopolymers to adsorb the heavy metal ions Cu²⁺ and Zn²⁺ from aqueous solutions was investigated. It was shown that as the concentration change (ΔC) increases, the sorption capacity increases; in most cases, the sorbent derived from dahlia tubers (DT) exhibits higher activity compared to Jerusalem artichoke (HT), which is associated with structural features and the availability of functional groups. Analysis of sorption isotherms showed that the adsorption of Cu²⁺ is well described by the Langmuir and Freundlich models, indicating a mixed sorption mechanism, whereas the Freundlich model is more appropriate for Zn²⁺, reflecting the heterogeneity of the surface and the presence of active sites with different interaction energies. The obtained data confirm the potential of nanostructured pectin biopolymers as environmentally safe sorbents for the removal of heavy metals from aqueous media and serve as a basis for the development of new sorption materials.