Faecal coliform (FC) microorganisms are one of the most important indicators in water quality management, since their presence reveals the possibility of existence of other dangerous microorganisms, leading to higher health risks. An accurate estimate of the concentration of this indicator helps better evaluation of the water pollution in riverine basins; thus, it is essential for future developments. The FC mortality rate depends on the physical, chemical, and biological processes in rivers. These processes are generally affected by environmental conditions. In this study, the decay coefficient (K) or mortality rate are related to the environmental parameters such as temperature, turbidity, pH, and salinity by an empirical equation. The results showed that turbidity and temperature are the most effective parameters. Moreover, an empirical equation was developed utilizing numerical model calibration, which describes the relationship of the mortality rate (K) with water temperature and turbidity. This equation was then added to the water quality module of the FASTER numerical model. Comparison of the measured FC concentrations with the predicted values obtained from the numerical model showed that the model accuracy significantly improved for the dynamic and variable decay coefficient.