Nanochannel ion transport is known to be governed by surface charge at low ionic concentrations. In this paper, we show that this surface charge is typically dominated by hydronium ions arising from dissolution of ambient atmospheric carbon dioxide. Taking the hydronium ions into account, we model the nanochannel conductance at low salt concentrations and identify a conductance minimum before saturation at a value independent of salt concentration in the dilute limit. Via the Poisson-Boltzmann equation, our model self-consistently couples chemical-equilibrium dissociation models of the silica wall and of the electrolyte bulk, parametrized by the dissociation reaction constants. Experimental data with aqueous KCl solutions in 165-nm-high silica nanochannels are described well by our model, both with and without extra hydronium from added HCl.