Solvothermal reactions of dimethyl pyridazine-3,6-dicarboxylate and appropriate metal chlorides in the absence/presence of KCl, NaCl or NH₄Cl yielded a series of coordination compounds of pyridazine-3,6-dicarboxylate (pzdc) with Mn(II), Co(II), Ni(II) and Zn(II). All the Mn(II) compounds contain the anionic binuclear motif [Mn₂(pzdc)₃]²⁻ with the trigonal prismatic shape. Through the K/Na-O electrostatic coordination, charge-assisted N–H⋯O hydrogen bonds, and weak C–H⋯O hydrogen-bonds, the binuclear prismatic anion co-assembles with different cations ([Mn(H₂O)₆]²⁺, K⁺, Na⁺ or NH₄⁺) to generate 3D architectures. Under similar synthetic conditions, the Co(II) and Ni(II) ions always give the neutral binuclear molecules [M₂(pzdc)₂(H₂O)₄], which are self-assembled into 3D hydrogen-bonded networks. The Zn(II) ion seems to be amphibious: in the presence of NH₄⁺, K⁺ and Na⁺, it forms the [Zn₂(pzdc)₃]²⁻ species that are isostructural with the Mn(II) species, but the absence of the above cations leads to [Zn₂(pzdc)₂(H₂O)₄], which is isomorphous with the Co(II) and Ni(II) compounds. The different structures have been qualitatively explained based on the metal ionic size, ligand constraints, inter-ligand repulsion, ligand-field effects, and anionic–cationic interactions. Magnetic studies on selected Mn(II) compounds reveal that weak antiferromagnetic coupling is operative through the triple pyridazine bridges within the prismatic anions.