Residence time distribution (RTD) of liquid phase in a two-compartment (packed-bed/packed-bed or packed-bed/packing-free) bioreactor for wastewater treatment was evaluated via a complex liquid flow structure. RTD in packed-bed compartments was modelled using a modified axial dispersion-exchange model with a liquid stream which bypasses the dynamic liquid region. The liquid in the dynamic region is dispersed in axial and transverse directions, whereas the stagnant region exchanges mass with the dynamic region, the two regions being in direct contact. RTD in packing-free compartment was modelled as a continuous stirred-tank reactor with ideal or non-ideal mixing zone. Time-domain analysis coupled with the phenomenological RTD model was used to identify the model parameters. The proposed RTD model offers the opportunity to quantify parameters as dynamic liquid fraction, dynamic liquid flow rate fraction, number of transfer units between dynamic and stagnant liquid regions, stagnant liquid holdup, which otherwise would have been difficult to estimate using other methods and which can affect the bioreactor performance. The proposed RTD model describes adequately the hydrodynamics of the two-compartment packed-bed bioreactor while the simulations unveil likely tendency of the RTD curves subject to different sets of model parameters.