South Africa has developed a policy and law that calls and provides for the equitable and sustainable use of water resources. Sustainable resource use is dependent on effective resource protection. Rivers are the most important freshwater resources in the country, and there is a focus on developing and applying methods to quantify what rivers need in terms of flow and water quality. These quantified and descriptive objectives are then related to specified levels of ecological health in a classification system. This paper provides an overview of an integrated and systematic methodology, where, fer each river, and each river reach, the natural condition and the present ecological condition are described, and a level/class of ecosystem health is selected. The class will define long term management goals. This procedure requires each ecosystem component to be quantified, starting with the abiotic template. A modified flow regime is modelled for each ecosystem health class, and the resultant fluvial geomorphology and hydraulic habitats are described. Then the water chemistry is described, and the water quality changes that are likely to occur as a consequence of altered flows are predicted. Finally, the responses to the stress imposed on the biota (fish, invertebrates and vegetation) by modified flow and water quality are predicted. All of the predicted responses are translated into descriptive and/or quantitative management objectives. The paper concludes with the recognition of active method development, and the enormous challenge of applying the methods, implementing the law, and achieving river protection and sustainable resource-use.