AnoxAn is a novel multi-environment reactor for biological nutrient removal (BNR) from wastewater. Although its biological efficacy has been demonstrated on a pilot scale, hydrodynamics is observed to significantly affect the performance of AnoxAn. To study its complex hydraulic behaviour, a model based on Computational Fluid Dynamics 3D (CFD) is constructed using the OpenFOAM® open source toolbox and validated by experimental tests of Residence Time Distribution (RTD). Reactor elements represent a key factor in the modelling process. In this sense, the impeller of the anoxic zone is modelled as a flat disk, and the baffle after the anoxic zone as a porous media. According to CFD model simulations, stagnant, short-circuit zones and mixing quality are established and quantified. Finally, the influence on the hydrodynamics of reactor elements is also evaluated. The results of this detailed hydrodynamic analysis will form the basis for the design and optimization of scalable AnoxAn configurations.