This paper investigates the mixing phenomena in pipe junctions in water distribution systems. Network simulation models frequently assume that mixing at pipe junctions is complete and instantaneous. In the present study, a series of experiments using tee and cross junctions with varying inflows and free chlorine concentrations were carried out in the Hydraulic Laboratory of the Institute of Engineering at the National Autonomous University of Mexico. Numerical simulations of these experiments were also performed using EPANET-BAM. Experimental results from this study showed that mixing is not complete in most of the cases; intersecting flows tend to bifurcate rather than mix completely. Numerical simulations indicated good agreement between calculated and measured values. The model was also tested using data from the water distribution system of Duberger-Les Saules, in Quebec City, Canada. A larger vulnerability zone was identified due to the impact of the incomplete mixing at the cross junction in the prediction of chlorine residual in a water distribution network.