Polarizable interaction potentials, parametrized using ab initio electronic structure calculations, have been used in molecular dynamics simulations to study the effect of cation composition on the ionic conductivity in the Zr(2)Y(2)O(7)-Y(3)NbO(7) system and to link the dynamical properties to the degree of lattice disorder. Across the composition range, this system retains a disordered fluorite crystal structure and the vacancy concentration is constant. The observed trends of decreasing conductivity and increasing disorder with increasing Nb(5+) content were reproduced in simulations with the cations randomly assigned to positions on the cation sublattice. The trends were traced to the influences of the cation charges and relative sizes and their effect on vacancy ordering by carrying out additional calculations in which, for example, the charges of the cations were equalized. The simulations did not, however, reproduce all of the observed properties, particularly for Y(3)NbO(7). Its conductivity was significantly overestimated and prominent diffuse scattering features observed in small area electron diffraction studies were not always reproduced. Consideration of these deficiencies led to a preliminary attempt to characterize the consequence of partially ordering the cations on their lattice, which significantly affects the propensity for vacancy ordering. The extent and consequences of cation ordering seem to be much less pronounced on the Zr(2)Y(2)O(7) side of the composition range.