Abstract Large cities, such as Melbourne, generate substantial quantities of sewage, which, after treatment, must be disposed. Melbourne's sewage is disposed via two routes, that treated at the Western Treatment Plant (WTP) is discharged in enclosed Port Phillip Bay, while the Boags Rock outfall empties into the exposed Bass Strait. In Port Phillip Bay biogeochemical processes control the fate of waste, while in the Bass Strait physical mixing rapidly disperses the waste. These different processes require very different ecosystem models. Port Phillip Bay requires detailed modelling of water-column and in-sediment processes, in particular detailed models of recycling processes, and also modelling of benthos–water-column interactions. Interaction of these components gives the model a nonlinear response to change in load. The Bass Strait ecosystem model is simple with no modelling of the sediment and limited modelling of water-column recycling. This model's behaviour is largely controlled by the physical environment.