The effect of electrochemical potential on the behavior of electrochemically deposited Au-Ag-Au bimetallic atomic scale junctions (ASJs) is addressed here. A common strategy for ASJ production begins with overgrown nanojunctions and uses electromigration to back-thin the junction. Here, these steps are carried out with the entire junction under electrochemical potential control, and the relationship between junction stability and applied potential is characterized. The control of electrochemical potential provides a reliable method of regulating the size of nanojunctions. In general, more anodic potentials decrease junction stability and increase the rate at which conductance decays. Conductance behavior under these labile conditions is principally determined by Ag oxidation potential, electrochemical potential-induced surface stress, and the nature of the adsorbate. Junctions fabricated at more cathodic potentials experience only slight changes in conductance, likely due to surface atom diffusion and stress-induced structural rearrangement. Electrochemical potential also plays a significant role in determining adsorption-desorption kinetics of surface pyridine at steady state at Au-Ag-Au ASJs, as revealed through fluctuation spectroscopy. Average cutoff frequencies increase at more anodic potentials, as does the width of the cutoff frequency distribution measured over 80 independent runs. Three reversible reactions--pyridine adsorption, Ag atom desorption, and Ag-pyridine complex dissolution--can occur on the surface, and the combination of the three can explain the observed results.