Many rivers are increasingly threatened by extreme floods, and effective strategies for flood risk mitigation are difficult to pursue, especially in highly urbanized areas. A flexible and multipurpose use of the complex networks of artificial channels that typically cross these regions can play a role in flood risk mitigation. A relevant example concerns the possible completion of a waterway from Padova to the Venice Lagoon, in North-Eastern Italy. Once completed, the waterway can boost shipping (which is considerably more climate and environment friendly than road transport), can lead to a urban re-composition of the territory and, serving as a diversion canal for the Brenta River, can reduce hydraulic hazard as well. The goal of the present work was to assess this last point. To this purpose, the 2DEF hydrodynamic model was used to reproduce the complex Brenta–Bacchiglione river network. This network includes river reaches, diversion canals, bed sills, pump stations, and control structures that assures the proper operation of the system in case of flood events. The mixed Eulerian–Lagrangian, semi-implicit formulation of the model provided accurate and computationally efficient results for subcritical regimes. The model results showed that the waterway can divert a significant part of the Brenta floodwaters toward the Venice Lagoon, thus reducing flood hazard in the Brenta River downstream of Padova. The benefits also extend to the Bacchiglione River, whose floodwaters can be diverted into the Brenta River through an existing flood canal; indeed, the waterway withdrawal produces a drawdown profile in the Brenta River that allows diverting larger flow rates from the Bacchiglione River as well. Finally, by conveying the sediment-laden floodwaters of the Brenta River within the Venice Lagoon, the waterway could contribute to counteract the generalized erosion affecting the lagoon.