We analyse the impact of ship traffic in the vicinity of navigation channels in a wide shallow waterbody. The crucial hydrodynamic driver in this situation is the depression (Bernoulli) wake that may be transferred into a long-living solitary wave of depression over the shoals. The analysis considers navigation channels in the Venice Lagoon using a new large dataset of approximately 600 measured wake events associated to specific ships whose data are provided by the AIS system. Since the development of the modern industrial port and the opening of the Malamocco–Marghera channel in the late 1960s, growing pressure on the lagoon caused by ship traffic has raised concerns about its physical integrity and habitat survival. The transit of large vessels has been shown to have serious impacts on the shallow water areas adjacent to waterways. Depression wakes created by such vessels can reach significant dimensions (water level dropdown of up to 2.45 m at the channel margin), causing unusually large retreat rates of several sections of the shoreline and which may adversely affect the lagoon morphology. The wakes are analysed in relation to ship and morphological parameters. A formulation is proposed to predict wake amplitude on the basis of ship characteristics and motion.