We report on the first multi-epoch, phase referenced VLBI observations of the water maser emission in a high-mass protostar associated with a disk-jet system. The source under study, IRAS 20126+4104, has been extensively investigated in a large variety of tracers, including water maser VLBA data acquired by us three years before the present observations. The new findings fully confirm the interpretation proposed in our previous study, namely that the maser spots are expanding from a common origin coincident with the protostar. We also demonstrate that the observed 3-D velocities of the maser spots can be fitted with a model assuming that the spots are moving along the surface of a conical jet, with speed increasing for increasing distance from the cone vertex. We also present the results of single-dish monitoring of the water maser spectra in IRAS 20126+4104. These reveal that the peak velocity of some maser lines decreases linearly with time. We speculate that such a deceleration could be due to braking of the shocks from which the maser emission originates, due to mass loading at the shock front or dissipation of the shock energy.