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[Abstract:] This paper presents a new freeware simulation tool (IberWQ) for 2D water quality modelling in rivers and non-stratified estuaries. The model computes the spatial and temporal evolution of several species and variables which are relevant for the evaluation of the environmental status of rivers and estuaries, including: Escherichia coli, dissolved oxygen, carbonaceous biochemical oxygen demand, organic nitrogen, ammoniacal nitrogen, nitrate–nitrite nitrogen, water temperature and salinity. A depth-averaged transport equation is solved for each variable with a mass conservative unstructured finite volume solver. IberWQ is fully coupled to the hydrodynamic module of the software Iber, a freeware simulation tool for solving the 2D shallow water equations. Both models are integrated in the same windows graphical environment, including several tools which allow the user to generate unstructured meshes adapted to the site topography, define spatially variable input parameters and visualize model outputs. We present four application examples to illustrate the possibilities of the software for the dynamic simulation of water quality in rivers and estuaries.