Gallium arsenide coating by molecular layers is a of increasing interest both for its surface passivation and for its use as a chemical or biochemical sensor. The surface state of GaAs and the nature of the molecular functionality to be bound to the surface are very important to assure good and durable adhesion. This work, using both the vibrational and the electronic energy loss range of high resolution electron energy loss spectra, showed that the water content in the solvent – acetonitrile – has a dramatic effect on the amount of phenylphosphonic acid molecules adsorbed on the GaAs substrate. There is a poor molecular adsorption for water contents ranging from 0 to 4% volume: HREELS spectrum is always a combination of the substrate and the adsorbed molecule spectra. For a water content of 5% there is an abrupt jump in the HREELS spectra shape: they become typical of phenyl groups in the electronic region. In the vibrational region, the typical C-H stretching peaks of aliphatic chains disappear showing that the extreme surface is exclusively covered by phenyl functions. Also for the samples, where a large adsorption occurs, surfaces become negatively charged under electron irradiation showing the existence of a large number of traps for incident electrons. Sonication of such well covered substrates destroys intermolecular bonds but keeps molecules that are chemically bound to the substrate.