An alternative approach for combined water treatment as opposed to its CSO discharge into receiving water is its bypass to the inlet of secondary clarifiers (SC). To analyse the processes and to evaluate the performance of this approach, experiments and numerical modelling were carried out. In batch and pilot scale experiments major effects were identified and quantified. The Activated Sludge Model No. 3 (ASM3) was modified to simulate the batch and pilot scale experiments for implementation of the bypass-specific processes and thus to set up an overall balance of the relevant compounds. With some modifications of ASM3, good agreement of the modelling results with measurements of COD, nitrogen and phosphorus were achieved.