A rapid process of water reform in Australia has seen governments rely heavily on ‘expert’ or ‘scientific’ panel advice for river condition and environmental flow assessments. These multi-disciplinary teams of scientists have enabled a quick and relatively inexpensive injection of science into what is often a data-poor decision process. However, expert panels suffer from several important drawbacks including a lack of transparency and repeatability, and unquantified uncertainty. In the case of the Snowy Mountains hydro-electric scheme, a government initiative to corporatize the government-owned authority led to the establishment of the Snowy Water Inquiry (SWI) that was required by law to propose and evaluate (within a six month period) a range of options for future river regulation, diversion and environmental flows. A Scientific Reference Panel (SRP) was therefore established to assess current (1998) river condition and to assess the likely environments benefits of a range of environmental flow options. The SRP attempted to overcome a number of the typical shortcomings of the expert panel approach by (i) integrating available data with expert opinion in its assessments, and (ii) developing a composite River Condition Index (RCI) underpinned by a conceptual framework that links habitat and biotic condition and comprises several sub-indices that translate qualitative assessments (relative to a pre-disturbance reference condition) into numeric values in a transparent and repeatable manner. The SRP estimated the level of uncertainty associated with its various assessments, and used these to quantify uncertainty estimates on RCI values. In this paper the RCI is described and its use is illustrated through presentation of the assessments of current (1998) river condition and the associated uncertainty analyses that were made for the rivers in the Snowy Mountains area. The results suggest that in spite of high levels of uncertainty associated with individual assessments, the SRP was able to demonstrate significant difference in current condition between rivers, and in likely future condition between different environmental flow scenarios. Although further investigations and lengthy negotiations occurred subsequent to the SWI to achieve corporatization, the environmental assessments made in the SWI provided the most comprehensive source of information available to governments and the community regarding the likely environmental outcomes of the proposed changes. Subsequent to the SWI the scenario-based approach to environmental flow assessment has become increasingly common internationally, and major Australian river condition assessments have adopted a similar conceptual framework to the RCI. Copyright © 2004 John Wiley & Sons, Ltd.