Investment in water infrastructure and management can enhance the ecological health of water-dependent ecosystems along highly regulated rivers. Investment in new flow-control infrastructure and management of both existing and new infrastructure can help return natural environmental flows to achieve healthy and representative areas of river ecosystems. In this paper, we developed an integrated model to cost-effectively restore environmental flows and ecosystem health in the River Murray in South Australia. The model integrates a range of hydrological, ecological, economic, and social components. A hydrological model is used to identify spatial and temporal inundation dynamics given flow rates and weir operation. Ecological response models were developed to link three aspects of environmental flows (flood duration, timing, and interflood period) to the health responses of ecosystem components. The infrastructure investments (flow-control regulators and irrigation pump relocation) were sited by interpreting high resolution LiDAR elevation data, digital orthophotography, and wetland mapping information; and their costs were quantified using a spreadsheet-based model. Social values were also estimated using a choice model quantifying willingness to pay for various ecosystem components and these were also included in the model. These diverse datasets and models were integrated in a decision support tool based on non-linear integer programming to investigate the cost-effectiveness of alternative flow levels and timing, existing flowcontrol infrastructure operation, and new infrastructure investment alternatives, given wider system constraints. The decision support tool can identify a suite of cost-effective infrastructure investments and a plan for their operation specifying where and when to capture and release water in riparian ecosystems. Outputs include a ranking of investment alternative and rules for managing flow-control infrastructure to achieve ecological and social values at minimum economic cost. In this paper we discuss the development and integration of the range of hydrological, ecological, economic, and social components of the model and the objectives of integrated river ecosystem management.