Objectively assessing ecological benefits of competing watering strategies is difficult. We present a framework of coupled models to compare scenarios, using the Coorong, the estuary for the MurrayDarling River system in South Australia, as a case study. The framework links outputs from recent modelling of the effects of climate change on water availability across the MurrayDarling Basin to a hydrodynamic model for the Coorong, and then an ecosystem-response model. The approach has significant advantages, including the following: (1) evaluating management actions is straightforward because of relatively tight coupling between impacts on hydrology and ecology; (2) scenarios of 111 years reveal the impacts of realistic climatic and flow variability on Coorong ecology; and (3) ecological impact is represented in the model by a series of ecosystem states, integrating across many organisms, not just iconic species. We applied the approach to four flow scenarios, comparing conditions without development, current water-use levels, and two predicted future climate scenarios. Simulation produced a range of hydrodynamic conditions and consequent distributions of ecosystem states, allowing managers to compare scenarios. This approach could be used with many climates and/or management actions for optimisation of flow delivery to environmental assets.