This paper outlines the derivation of spatially-based models for fish-based assessment of the ecological status of rivers in England and Wales. The analysis highlights the key steps in the approach to develop such tools. For each step a number of alternative approaches were tested, and for each approach the major limitations and problems identified. This development of a multi-metric index in England and Wales indicated that, whilst the approach does provide promising results for the future, at this stage index development is constrained by limited data for some parts of the analysis. These mainly relate to coping with the zoogeographical influence of species distribution in a descriptive river typology, the availability of data for variables that adequately predict reference fish community types for impacted sites and availability of sufficient sites at a range of ecological conditions with which to test metrics and build an index that can be used to support implementation of the European Union Water Framework Directive.