Complex formation in systems containing manganese (II), natural pectin and/or pectin modified by organic pharmacophores (nicotine, salicylic, 5-aminosalicylic, anthranilic acids) was studied by spectral (UV-, IR-, NMR 13C spectroscopy), potentiometric and viscometric methods. Method isomolar series and the molar relationship defined by the molar composition and the range of stability of metal complexes: pectin + nicotinic acid > pectin + acid 5-aminosalicylic > pectin + anthranilic acid > pectin + salicylic acid > native pectin. It is shown that the stability constant of metal complexes is significantly influenced by the reaction temperature and the structure of the pharmacophore. The presence of an amino group in the structure of an aromatic molecule increases the stability of metal complexes by 1.5–2 orders of magnitude. The standard thermodynamic characteristics (∆Hº; ∆Gº; ∆Sº) are calculated, which indicate that the processes of complexation in all cases are enthalpy-entropy favorable (∆Hº<0, ∆Sº>0) and proceed spontaneously (∆Gº<0). The influence of the structure of the drug compound in the polymer ligand on a number of physical and chemical properties of metal complexes was revealed. The data of NMR 13C and IR-spectra allow us to conclude that not only carboxyl groups but also hydroxyl functions of polymer matrices participate in the coordination interaction of pectin and/or pharmacophore-containing pectin with manganese (II) cations.