A polar cobalt(II) phosphonate Co(bamdpH(2))(H2O) (1) [bamdpH(4) = (benzylazanediyl)bis(methylene)diphosphonic acid] is reported. It shows a linear chain structure. The neighboring chains are connected by moderately strong hydrogen bonds forming a supramolecular layer. The interlayer spaces are filled with the organic groups of the phosphonate ligands. Compound 1 displays the coexistence of single-chain magnet behavior and canted antiferromagnetism below 2.8 K. Moreover, the magnetic dynamics is strongly dependent on the synthetic methods, a phenomenon that has not been documented before.