Stream invertebrate assemblages are the product of multiple-scale habitat filters and a major goal in community ecology is to determine which scales most influence the relationships between habitat and assemblage structure. We analyzed the relationships between habitat and the functional structure of invertebrate assemblages at three spatial scales (microhabitat, stream-reach, basin), using 264 samples collected in 38 French stream reaches in two basins. The habitat was described in terms of hydraulic conditions (Froude number), substrate size and benthic particulate organic matter. The functional structure of assemblages was described by 60 categories of 12 biological traits of invertebrates. At the microhabitat scale (within reaches), relationships between habitat and traits were significant for 96 out of 180 tests (R2 up to 26%). At the reach scale (within basins), habitat-trait relationships were significant for 46 out of 180 tests (R2 up to 34%); reach-scale effects did not differ between the two basins. Between basins, 34 out of 60 trait categories differed (R2 up to 62%). For all traits except three (body flexibility, number of reproductive cycle per year and respiration patterns), habitat-trait relationships at the microhabitat and reach scales were consistent: maximum size, form of the body, attachment to the substrate, feeding habits, reproduction techniques, life duration and strategies of dissemination were significantly related with habitat variables, especially with hydraulics. These results reflected sensitive adaptation to contrasted habitat characteristics in terms of resistance to drag and foraging strategies. However, overall differences between basins were inconsistent with patterns observed at smaller scales. Therefore, microhabitat selection can be upscaled to partly explain functional variability across reaches, but effects of other filters at the reach or larger scales should be further studied to improve our understanding of invertebrate community structure.