Rigorous modeling of transport phenomena is essential to reproduce accurately biofiltration systems performance. In this sense, the aim of this study was to investigate the effect of integrating fluid flow dynamics in the development of these bioreactor models, mimicking their hydrodynamics and behavior in a fixed biofilm reactor. 2D bioreactor models were developed using three, different well-established tools for modeling bioreactors (AQUASIM, MATLAB, and Computational Fluid Dynamics - CFD), considering from ideal flow patterns to more complex fluid dynamics. A detailed comparison was performed among the results, taking into account the simulation of dissolved oxygen profiles in the liquid phase, inside the biofilm and in the boundary layer along a bioreactor. These models were validated by comparing the simulations with direct measurements obtained by means of dissolved oxygen microsensors of high spatial resolution. In all cases, deviations were below 6%, nevertheless CFD predictions obtained the lowest deviations below 3.5%. Thus, these results underline that CFD techniques are appropriate to model more accurately the performance of fixed-bed biofilm reactors, allowing the study in detail of all the hydrodynamics variables involved in the process. In addition, a 3D CFD model, combining hydrodynamics and biological reactions, was developed and solved to simulate local transient flow and dynamic behaviors of oxygen consumption in the bioreactor. The results of CFD simulations were evaluated in order to know the effect of mass transport phenomena (advection and diffusion) by characterizing hydrodynamics and, finally, to predict the oxygen degradation along the bioreactor. (C) 2016 Elsevier B.V. All rights reserved.