In 2011, the Australian government proposed the Murray-Darling Basin Plan to promote a healthy working river system. The proposed Plan seeks to limit surface water (consumptive) use to 10873 GL/year on a long-term average. The controversy prompted by this proposed reduction in extractive allocations has underscored the need for transparent and objective modelling of ecological benefits. In this paper, we investigate the likely ecological outcomes of the proposed plan for the Macquarie Marshes, a Ramsar-listed wetland in the Murray-Darling Basin, using a decision support system (DSS). The DSS uses a detailed wetland hydrological model to drive ecological responses for a range of important species. Our hydrological modelling results indicate that the proposed plan would increase inundation extent significantly with a 33% increase for the median when compared with the current water sharing plan. The increase in inundation extent would improve the hydrologic condition in most wetlands. Our ecological modelling results show that the improved hydrology would enhance the wetland quality for a range of vegetation and water-bird species, although benefits are not distributed evenly across the wetlands. For a number of species, some wetlands within the marshes have habitat quality scores matching the predevelopment scenario and benefits of additional environmental water allocation were noticeable when modelled for a prolonged drought period.