In Water Distribution Networks (WDN), the water quality could become vulnerable due to several operational and temporal factors. Epanet is a hydraulic and water quality simulation software, widely used, to preserve the control of chemical disinfectants in WDN among other capabilities. Several researchers have shown that the flow mixing at Cross-Junctions (CJs) is not complete as Epanet assumes for the cases of two contiguous inlets and outlets. This paper presents a methodology to obtain the outlet concentrations in CJs based on experimental scenarios and a validated Computational Fluid Dynamics (CFD) model. In this work, the results show that the Incomplete Mixing Model (IMM) based on polynomial equations, represents in a better way the experimental scenarios. Therefore, the distribution of the concentration could be in different proportions in some sectors of the network. Some comparisons were made with the complete mixing model and the Epanet-Bulk Advective Mixing (BAM), obtaining relative errors of 90% in some CJs.