By virtue of its magnetic moment and variable valencies, the D4h paddlewheel ruthenium dimer is a desirable molecular building block for the construction of functional networks. If in addition to the Ru open axial site the organic ligand is designed to allow transversal connections, a wider range of structural possibilities is expected. The organic ligand can also be modified to introduce other functionalities. In the present study we employed a diphosphonate containing a protonated amine, 1-ammoniummethylenediphosphonate [NH3CH(PO3)23-; (Hamdp)], as the ligand to construct paddlewheel Ru2(Hamdp)2 building block. Three networks of different structural dimensionalities were obtained. (H3O)2[RuII2(Hamdp)2] (1) forms one-dimensional chain of S = 1 RuII2 bridged at axial positions through Ru-O bonds. From 1 as a starting material, its reaction with lanthanide ions results in the bimetallic Dy(H2O)3[Ru2(Hamdp)2][Ru2(Hamdp)2(H2O)2][Ru2(Hamdp)(amdp)]0.5·12H2O (2), which has a pillared-bilayer structure and Yb[Ru2(Hamdp)2]2[Ru2(Hamdp)2(H2O)2]·15H2O (3), which is a three-dimensional open framework, both contain mixed-valent RuII/III2 units and show new connection topologies of the Ru2 dimers. After activation 2 does not adsorb N2 and CO2 but takes up 12 H2O. In contrast, 3 take up all three gases. The optimum proton conductivities were moderate reaching 1.44 × 10-6 for 2 and 0.93 × 10-5 S cm-1 for 3 at 95% relative humidity and 55 °C.