This paper presents CalHidra 3.0, a new software package developed for dynamic simulation of water quality in rivers. CalHidra 3.0 combines a 1-D hydrodynamic model based on Saint Venant equations, a transport sub-model that incorporates the advection-dispersion terms, and a simplified version of the River Water Quality Model 1 (RWQM1) for the biochemical transformations. This advanced biochemical sub-model allows the dynamic simulation of the bacterial populations in rivers, making possible the simulation of the river acclimatisation to changes of pollutant load or environmental conditions. The software also includes new tools for a Monte Carlo based Bayesian calibration of the unknown model parameters. CalHidra 3.0 is implemented based on the Component Object Model (COM) programming paradigm and uses the Windows graphical environment. Three case studies illustrate the possibilities of the CalHidra 3.0 software.