The use of trait-based approaches to examine the ecology of stream fish assemblages is increasing. However, selection of traits that will be useful in testing spatial or temporal hypotheses about ecological organisation is currently limited by availability of data, rather than empirical evaluation. 2. We analysed two data sets of stream fish assemblages to compare taxonomy and trait-based approaches. The Wabash River temporal data set is based on 25 years of boat electrofishing collections over a 230-km river distance. The Indiana Department of Environmental Management data set of stream collections in the state of Indiana was selected to represent a spatial database. We compared several trait-based approaches: reproductive guilds, life history variables, biomonitoring metrics, ecosystem-based functional guilds and feeding and ecosystem interaction guilds. 3. Analyses of fish assemblages that are designed to detect how environmental variation structures fish assemblages can expect similar results using taxonomic or trait-based approaches. Results of trait-based approaches will vary according to the spatial extent of the region and the number of unique entities of trait groups for a given data set. However, taxonomic analyses accounted for more variation than any trait-based analyses.