This work presents a theoretical mechanistic study of the protonation of pyridine in water clusters, at the B3LYP/cc-pVDZ theory level. Clusters from one to five water molecules were used. Starting from previously determined structures, the reaction paths for the protonation process were identified. For complexes of pyridine with water clusters of up to three water molecules just one transition state (TS) links the solvated and protonated forms. It is found that the activation energy decreases with the number of water molecules. For complexes of four and five water molecules two transition states are found. For four water molecules, the first TS links the starting solvated structure with a new, less stable, solvated form through a concerted proton transfer between a ring of water molecules. The second TS links the new solvated structure to the protonated form. Thus, protonation is a two-step process. For the five water molecules cluster, the new solvated structure is more stable than the starting one. This structure exhibits two double hydrogen bonds involving the pyridinic nitrogen and several water molecules. The second TS links the new structure with the protonated form. Now the process occurs in one step. In all cases considered, the proton transfers involve an interconversion between covalent and hydrogen bonds. For four and five water molecules, the second TS is structurally and energetically very close to the protonated form. As evidenced by the vibration frequencies, this is due to a flat potential energy hypersurface in the direction of the reaction coordinate. Determination of DeltaG at 298.15 K and 1 atm shows that the protonation of pyridine needs at least four water molecules to be spontaneous. The complex with five water molecules exhibits a large DeltaG. This value yields a pKa of 2.35, relatively close to the reported 5.21 for pyridine in water.