Abstract The Murray–Darling Basin in Australia is severely environmentally degraded as a result of a range of anthropogenic changes, most notably the regulation and extraction of surface water resources for irrigated agriculture. Environmental problems include eutrophication of rivers and storages, elevated salinity levels, widespread blooms of toxic blue–green algae, decline of native fish and bird populations, and reduction of area of riverine wetlands. Both the community and the government are committed to improving the state of the environment in the Basin, both for it's intrinsic ecological values, and to ensure the sustainability of production in what is Australia's most economically important agricultural region. To facilitate the on-going trade-off process between competing users of this resource, a decision support system (DSS) is being developed which will enable explicit prediction of the likely response of key features of the riverine environment to proposed flow management scenarios. The DSS is being developed using the RAISON shell ( Lam, D.C.L., Mayfield, C.I., Swayne, D.A., Hopkins, K., 1994. A prototype information system for watershed management and planning. Journal of Biological Systems 2 (4), 499–517), and will integrate a range of simple models of riverine ecology which are being developed. These models will include qualitative and quantitative models representing the response of different aspects of the instream and floodplain ecology dependent upon the river flow regime. The DSS will not include a detailed model of river hydrology or hydraulics, but rather, will use the output from the range of such models currently in use in the Basin as inputs to the ecological models. The DSS will also provide a range of tools to allow user-defined evaluation of scenario results, as well as explanations and supporting information to elucidate the ecological modelling.