Polyoxometalates (POMs) are promising candidates for molecular electronic applications because (1) they are inorganic molecules, which have better CMOS compatibility compared to organic molecules; (2) they are easily synthesized in a one-pot reaction from metal oxides (MOx) (where the metal M can be, e.g., W, V, or Mo, and x is an integer between 4 and 7); (3) POMs can self-assemble to form various shapes and configurations, and thus the chemical synthesis can be tailored for specific device performance; and (4) they are redox-active with multiple states that have a very low voltage switching between polarized states. However, a deep understanding is required if we are to make commercial molecular devices a reality. Simulation and modeling are the most time efficient and cost-effective methods to evaluate a potential device performance. Here, we use density functional theory in combination with nonequilibrium Green’s function to study the transport properties of [W18O54(SO3)2]4–, a POM cluster, in a variety of molecular junction configurations. Our calculations reveal that the transport profile not only is linked to the electronic structure of the molecule but also is influenced by contact geometry and presence of ions. More specifically, the contact geometry and the number of bonds between the POM and the electrodes determine the current flow. Hence, strong and reproducible contact between the leads and the molecule is mandatory to establish a reliable fabrication process. Moreover, although often ignored, our simulations show that the charge balancing counterions activate the conductance channels intrinsic to the molecule, leading to a dramatic increase in the computed current at low bias. Therefore, the role of these counterions cannot be ignored when molecular based devices are fabricated. In summary, this work shows that the current transport in POM junctions is determined by not only the contact geometry between the molecule and the electrode but also the presence of ions around the molecule. This significantly impacts the transport properties in such nanoscale molecular electronic devices.