The synthesis, crystal structure, and magnetic behavior of nine transition-metal complexes based on pyrazine-2,5-dicarboxylato (pz25dc) and pyrazine-2,3-dicarboxylato (pz23dc) ligands are reported. The pz25dc ligand displays a bis-bidentate coordination mode, with the carboxylate groups almost coplanar with the pyrazine ring, to afford polymeric 1-D chains [Mn(1), Fe(2), Zn(3), and Cu(4 and 5)] and discrete dimeric entities [Mn(6)] when the 1,10-phenanthroline (phen) blocking ligand is used to avoid further polymerization. The nonplanar pz23dc ligand chelates to a unique copper center, while it bridges another one or two metal centers via the remaining carboxylate group, leading to 1-D polymeric chains (7), ladder chains (8), and sheets (9). The crystal packing of the metal-organic frameworks of compounds 4-9 generates voids which are occupied by assembled water molecules. The different water cluster patterns (tapes, four-membered discrete rings, and chains for compounds 6, 8, and 9, respectively) and their role in the cohesiveness of supramolecular architectures are analyzed. Thermogravimetric and variable-temperature X-ray powder diffraction studies have revealed the occurrence of reversible dehydration processes in compounds 6, 8, and 9. Furthermore, the magnetic behavior of these compounds has been studied in order to analyze the capability of the pyrazine ring to transmit magnetic interactions.