Tethered bilayer lipid membranes (tBLMs) are increasingly used in biosensor applications where electrochemical impedance spectroscopy (EIS) is the method of choice for amplifying and recording the activity of membrane-damaging agents such as pore-forming toxins or disrupting peptides. While the activity of these biological agents may depend on the pH of the analytes, there is increasing evidence that the sensitivity of tethered bilayer sensors depends on the pH of the solutions. In our study, we addressed the question of what are the fundamental reasons for the variability of the EIS signal of the tBLMs with pH. We designed an experiment to compare the EIS response of tBLMs with natural membrane defects and two different membrane disruptors: vaginolysin and melittin. Our experimental design ensured that the same amount of protein and peptide was present in the tBLMs, while the pH was varied by replacing the buffers with different pH values. Using a recently developed EIS data analysis algorithm from our research group, we were able to demonstrate that, in contrast to previous literature which relates the variability of tBLM, EIS response to the variation in defect density, the main reason for the observed variability in EIS response is the change in the sub-membrane properties of tBLMs with pH. Using surface-enhanced infrared absorption spectroscopy (SEIRAS), we have shown that pH changes from neutral to slightly acidic leads to an expulsion of water, presumably bound to ions, from the sub-membrane reservoir, resulting in a marked decrease in the carrier concentration and specific conductance of the sub-membrane reservoir. Such a decrease is recorded by the EIS as a decrease in the conductance of the tBLM complex and affects the sensitivity of a biosensor. Our data provide important evidence of pH-sensitive effects that should be considered in both the development and operation of biosensors.