Despite mass flow being arguably the most elementary transport associated with nanofluidics, its measurement still constitutes a significant bottleneck for the development of this promising field. Here, we investigate how a liquid flow perturbs the ubiquitous enrichment—or depletion—of a solute inside a single nanochannel. Using fluorescence correlation spectroscopy to access the local solute concentration, we demonstrate that the initial enrichment—the so-called Donnan equilibrium—is depleted under flow, thus revealing the underlying mass transport. Combining theoretical and numerical calculations beyond the classical 1D treatment of nanochannels, we rationalize quantitatively our observations and demonstrate unprecedented flow rate sensitivity. Because the present mass transport investigations are based on generic effects, we believe that they can develop into a versatile approach for nanofluidics.