This paper describes a fundamental challenge when using silicon oxide nanochannels for analytical systems, namely the occurrence of a strong proton release or proton uptake from the walls in any transient situation such as channel filling. Experimentally, when fluorescein solutions were introduced into silicon oxide nanochannels through capillary pressure, a distinct bisection of the fluorescence was observed, the zone of the fluid near the entrance fluoresced, while the zone near the meniscus, was dark. The ratio between the zones was found to be constant in time and to depend on ionic strength, pH, and the presence of a buffer and its characteristics. Theoretically, using the Gouy-Chapman-Stern model of the electrochemical double layer, we demonstrate that this phenomenon can be effectively modeled as a titration of the solution by protons released from silanol groups on the walls, as a function of the pH and ionic strength of the introduced solution. The results demonstrate the dominant influence of the surface on the fluid composition in nanofluidic experiments, in transient situations such as filling, and changes in solvent properties such as the pH or ionic strength. The implications of these fundamental properties of silicon oxide nanochannels are important for analytical strategies and in particular the analysis of complex biological samples.