With fluorescence correlation spectroscopy (FCS), the diffusion and concentration of proteins (wheat germ agglutinin) in a nanofluidic system are measured on a single molecule level. By increasing the ionic concentration, the Debye length of the electrical double layer (EDL) decreases altering the strongly enhanced surface interactions of charged proteins in nanochannels. A theoretical model of the transport of charged mole- cules in nanofluidics facilitates the design of future nanochannel applications.