The role of water in the proton transfer mechanism between the carboxylic and the amino group in tryptophan was studied through the direct, intramolecular reaction in presence of a continuum and the single water molecule mediated, intermolecular reaction in vacuum and in presence of a continuum. The introduction of the continuum reduced the activation barriers for the proton transfer from the neutral form and stabilized the zwitterion in both cases. The reaction force and the reaction electronic flux along the intrinsic reaction coordinate allowed in combination with a Natural Bond Order Analysis a more detailed description of the influence of water on the reaction mechanism. Represented as a continuum model, water reduced the energy required for bond reorganization and did not alter the first part of the intermolecular reaction, characterized through the approximation of the water molecule to the functional groups of the amino acid and a polarization of the system. The absence of a water molecule in the intramolecular proton transfer with continuum changed the reaction coordinate to a reduction of the angle between the functional groups of the amino acid leaving the energy required for bond formation unaffected. Thus, the smaller activation barrier obtained in the direct intramolecular proton transfer with continuum model in comparison to the water mediated reaction, originates from the energetically more favorable angle reduction in comparison the approximation of a water molecule.