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The advancement of experimental and computational resources has facilitated the use of computational fluid dynamics (CFD) models as a predictive tool for mixing behaviour in full-scale waste stabilization pond systems. However, in view of combining hydraulic behaviour with a biokinetic process model, the computational load is still too high for practical use. This contribution presents a method that uses a validated CFD model with tracer experiments as a platform for the development of a simpler compartmental model (CM) to describe the hydraulics in a full-scale maturation pond (7 ha) of a waste stabilization ponds complex in Cuenca (Ecuador). 3D CFD models were validated with experimental data from pulse tracer experiments, showing a sufficient agreement. Based on the CFD model results, a number of compartments were selected considering the turbulence characteristics of the flow, the residence time distribution (RTD) curves and the dominant velocity component at different pond locations. The arrangement of compartments based on the introduction of recirculation flow rate between adjacent compartments, which in turn is dependent on the turbulence diffusion coefficient, is illustrated. Simulated RTD's from a systemic tanks-in-series (TIS) model and the developed CM were compared. The TIS was unable to capture the measured RTD, whereas the CM predicted convincingly the peaks and lags of the tracer experiment using only a minimal fraction of the computational demand of the CFD model. Finally, a biokinetic model was coupled to both approaches demonstrating the impact an insufficient hydraulic model can have on the outcome of a modelling exercise. TIS and CM showed drastic differences in the output loads implying that the CM approach is to be used when modelling the biological performance of the full-scale system., (Copyright © 2011 Elsevier Ltd. All rights reserved.)