We report detailed atomistic simulations combined with high-fidelity conductance calculations to probe the structural origins of conductance fluctuations in thermally evolving Au-benzene-1,4-dithiolate-Au junctions. We compare the behavior of structurally ideal junctions (where the electrodes are modeled as flat surfaces) to structurally realistic, experimentally representative junctions resulting from break-junction simulations. The enhanced mobility of metal atoms in structurally realistic junctions results in significant changes to the magnitude and origin of the conductance fluctuations. Fluctuations are larger by a factor of 2-3 in realistic junctions compared to ideal junctions. Moreover, in junctions with highly deformed electrodes, the conductance fluctuations arise primarily from changes in the Au geometry, in contrast to results for junctions with nondeformed electrodes, where the conductance fluctuations are dominated by changes in the molecule geometry. These results provide important guidance to experimentalists developing strategies to control molecular conductance, and also to theoreticians invoking simplified structural models of junctions to predict their behavior. © 2013 American Chemical Society.