Habitat modelling results are extremely sensitive to the habitat suitability criteria (HSC) used in the simulations. HSCs are usually expressed as univariate habitat suitability curves, although such univariate approach has been long questioned, since overlooking interactions between hydraulic variables may misrepresent the complexity of fish behaviour in habitat selection. It could lead to adopt erroneous flow management decisions based on misleading results. Furthermore, the interactive effects of hydraulic variables on habitat selection may be driven by the structural features of the channel, which determine cover availability. Therefore, we compared brown trout habitat selection patterns through multivariate resource selection functions (RSFs) in structurally contrasting rivers to unveil the interactive effects of hydraulics and cover elements and their consequences in univariate HSC results. Microhabitat preferences of young-of-the-year (0+) trout were similar across fast and slow waters, meanwhile juvenile (1+) and adult (>1+) preferences significantly changed. RSFs for young-of-the-year trout were consistent with univariate results and did not differ among water types. However, RSFs for older trout varied among water types and revealed complex interactions among hydraulic variables and between hydraulics and structural elements, which were not described accurately by univariate curves. Therefore, results suggest that interactions between water depth and current velocity have a significant effect on habitat selection patterns in juvenile and adult brown trout, this effect being controlled by cover availability. Copyright © 2008 John Wiley & Sons, Ltd.