In networks of rivers or humanmade canals (e.g. for drainage or irrigation, but also in streetpatterns during urban floods) junctions are ubiquitous, where different free surface flows merge or where one flow splits in two or more others. The complex and three-dimensional flox in such junctions does not only govern the transport through the network of dissolved or suspended matter (nutrients, pollutants, sediments) and the associated bed evolution (due to erosion and sedimentation), but also induces extra flood risks. Indeed, the head losses and the flow contraction in the junctions cause backwater effects (i.e. increased water elevations upstream of the junctions). By means of 3D numerical modelling, analytical modelling and lab-experiments, contributions will be made to the more accurate prediction of such backwater effects.