A new copper(II) phosphonatobenzenesulfonate incorporating 4,4'-bipyridine (4,4'-bipy) as auxiliary ligand has been discovered through systematic high-throughput (HT) screening of the system Cu(NO3)(2)center dot 3H(2)O/H2O3PC6H4SO3H/4,4'-bipy using different solvents. The hydrothermal synthesis of [Cu(HO3PC6H4SO3)(C10H8N2)]center dot H2O (1) was further optimized by screening various copper(II) salts. The crystal structure of 1 was determined by single-crystal X-ray diffraction and unveiled the presence of isolated sixfold coordinated Jahn-Teller-distorted Cu2+ ions. The isolated CuN2O4 octahedra are inter-connected by phosphonate and sulfonate groups to form chains along the c-axis. The organic groups, namely phenyl rings and 4,4'-bipy molecules cross-link the chains into a three-dimensional framework. Water molecules are found in the narrow voids in the structure which are held by weak hydrogen bonds. Upon dehydration, the structure of 1 undergoes a phase transition, which was confirmed by TG measurements and temperature dependent X-ray powder diffraction. The new structure of 1-h was refined with Rietveld methods. Detailed inspection of the structure revealed the directional switching of the Jahn-Teller distortion upon de/rehydration. Weak ferro-/ferrimagnetic interactions were observed by magnetic investigations of 1, which switch to antiferromagnetic below 3.5 K. Compounds 1 and 1-h are further characterized by thermogravimetric and elemental analysis as well as IR spectroscopy.