Alginate is a natural polymer widely applied in materials science, medicine, and biotechnology. Its ability to bind metal ions in order to form insoluble gels has been comprehensively used to create capsules for cell technology, drug delivery, biomedical materials, etc. To modify and predict the properties of cross-linked alginate, knowledge about the mechanism of alginate binding with metal ions and the properties of its gels is necessary. This article presents the results obtained by proton Nuclear Magnetic Resonance Spectroscopy for alginate containing calcium and strontium (alkaline earth metal diamagnetic) ions and by Electron Paramagnetic Resonance Spectroscopy for alginate with copper (Cu) and manganese (Mn) (transition metal paramagnetic) ions. It was found that in the case of calcium (Ca) and Mn ions, their concentration does not affect their distribution in the alginate structure and the cross-linking density. In the case of strontium (Sr) and Cu ions, their number affects the number of binding sites and, accordingly, the cross-linking density. Thus, the cross-linking of alginate depends mainly on the characteristics of specific cations, while the nature of the bond (ionic or coordination type) is less important.