We report the results from a six-year, multi-epoch very long baseline interferomertry monitoring of the Seyfert galaxy NGC3079. We have observed NGC3079 during eight epochs between 1999 and 2005 predominantly at 5GHz, but covering the frequency range of 1.7GHz to 22GHz. Using our data and observations going back to 1985, we find that the separation of two of the three visible nuclear radio components underwent two decelerations. At the time of these decelerations, the flux density of one of the components increased by factors of five and two, respectively. We interpret these events as a radio jet component undergoing compression, possibly as a result of a collision with ISM material. This interpretation strongly supports the existence of jets surrounded by a clumpy medium of dense clouds within the first few parsecs from the central engine in NGC3079. Moreover, based on recently published simulations of jet interactions with clumpy media, this scenario is able to explain the nature of two additional regions of ageing synchrotron material detected at the lower frequencies as by-products of such interactions, and also the origin of the kpc-scale super bubble observed in NGC3079 as the result of the spread of the momentum of the jets impeded from propagating freely. The generalization of this scenario provides an explanation why jets in Seyfert galaxies are not able to propagate to scales of kpc as do jets in radio-loud AGN.