A major drawback limiting the use of trickle-bed bioreactors for biological wastewater treatment is ascribed to the concomitant biological clogging and physical plugging phenomena induced, respectively, by the formation of an excessive amount of biomass and the retention of inert suspended fine particles advected in the liquid influent stream. Biomass growth and fine particles deposition permanently reshape the bed pore structure and narrow the free interstitial space left to the fluids flow thus occasioning progressive bed obstruction often accompanied with pressure drop build-up for the cocurrent gas–liquid flows taking place in trickle-bed biofilters. In these circumstances, for maintaining acceptable operating cycles, the unit must be backwashed and/or shutdown regularly for removing the excess biomass and for cleaning from the specific solid deposit. A predictive two-dimensional dynamic model linking the two-phase flow hydrodynamics to the space-time distribution of bioclogging/biokinetics and of inert fine particles deposition via deep-bed filtration in trickle-bed bioreactors for wastewater treatment was developed. The model was based on the volume-average mass and momentum balance equations for the gas and liquid phases and continuity equation for the solid phase, the volume-average species balance for the fine particles, simultaneous transport and consumption of substrate (pollutant) and oxygen within the biofilm and collecting solid particle, and the volume-average species balance equations in the liquid and gas phases. Phenol biodegradation by Pseudomonas putida as the predominant species immobilized on activated carbon was chosen as a case study to illustrate the incidence of biomass accumulation on trickle-bed bioreactor hydrodynamics.