<h2>Summary</h2> To predict many proton-involved reactions in natural and engineered systems, a better understanding of the difference between the solution pH in nanopores and the pH in the bulk solution is critical. However, how the pH in nanopores changes in response to changes in the bulk solution composition remains elusive. Here, the capability of surface-enhanced Raman scattering spectroscopy to measure both pH and ion concentrations enables us to discover a new mechanism: opposite ionic surface propensities induce differences in aqueous concentration and control the pH in nanopores. As further confirmed by our modified Poisson-Boltzmann model, in negatively charged nanopores, anion concentrations are still enhanced, whereas cation concentrations are suppressed. These effects can change the buffer's conjugated acid and base ratio and attract protons to compensate for the excess negative charge in nanopores. Collectively, compared with the bulk solution pH, these factors cause an unexpectedly low pH in nanopores.