In electroanalytical measurements, nanoporous glass plugs are widely used to contain the electrolyte solution that forms a salt bridge between the sample and the reference electrode. Even though reference electrodes with plugs made of nanoporous glass (such as Vycor or CoralPor glass) are commercially available and are frequently used, the limits of their use have not been explored thoroughly. It is shown here that at ionic strengths lower than 100 mM, the half-cell potentials of reference electrodes with nanoporous glass plugs are not sample independent, as it would be desirable, but they depend on the ionic sample composition. Sample dependent shifts of more than 50 mV in the half cell potential were encountered. Reference potentials were found to be affected in aqueous solutions by HCl, NaCl, KCl, and CaCl2 and in acetonitrile by CF3COOH and the supporting electrolyte tetrabutylammonium perchlorate. These observations cannot be explained by the liquid junction potential between two mutually miscible electrolyte solutions, as commonly described with the Henderson equation. Instead, they result from the surface charge density on the glass surface and the resulting electrostatic screening of ion transfer into the glass pores when the latter have dimensions comparable to or smaller than the Debye length. Users of reference electrodes with nanoporous glass plugs need to be aware of these limitations to avoid substantial measurement errors.