Sustainable management of natural resources is a well-accepted concept, but there are few practical guidelines for its application. This paper suggests methods for the sustainable operation of water resource use and protection. Environmental flows (EF) for rivers are used to illustrate some of the opportunities and problems inherent in managing rivers sustainably. In particular, there is a requirement for agreeing on clear and measurable environmental objectives for which a modified flow regime can be set. Knowledge from a number of different disciplines, including hydrology, ecology, hydraulics, geomorphology, water quality and socio-economics has to be integrated to provide holistic levels of understanding if sustainable management is to be achieved. Methods for EF assessment have been developed to provide an effective framework for integration leading to a clear end-point. The implementation of EF has been hampered in the past by a concentration on the ecohydrological technicalities of the process. More recently, it has been realized that achieving a consensus in the socio-economic and political context is of overriding importance for successful implementation. Case studies from South African river research over the past 20 years are used to illustrate the policies, methods, impediments and successes of sustainable river management. In particular, a recognition of complexity and change, both in ecosystems and in human thinking and behaviour, is emphasized. Timeframes of decades are required for both types of change, but there is evidence that patience is being rewarded by gradual success.