The intensification of agriculture has drastically modified the structure of rural landscapes, changing field size, destructing hedgerow networks, and increasing nutrients and fine sediments fluxes to rivers. To evaluate the effects of these disturbances at the catchment scale, we studied the surface and interstitial water chemistry and the invertebrate assemblages in three different habitats: the vegetation, the benthic, and the interstitial. Six headwater streams ranging from undisturbed to disturbed forests (wind-fallen area) and from traditional agriculture to intensive farming areas were studied. Differences between forested and agricultural streams lie in changes in water chemistry, in habitat quality, and in the composition of the assemblages with little reduction in species richness. The forested streams were only disturbed by large-scale modifications of their catchments (i.e. wind-fallen area along the stream), which made the invertebrate assemblages similar to those of agricultural streams, even if water characteristics were not modified. In contrast, large scale modifications of landscape structure near the agricultural streams (hedgerow removal) had little effect on the fauna, but the destruction of the riparian strip (with direct access of the cattle to the river) profoundly affected the system with drastic modifications of in-stream habitat quality and invertebrate assemblage composition. The effects of these disturbances differed according to the habitat considered, with increasing differences between assemblages from the interstitial, to the benthic, and to the vegetation habitats. Finally, groups of organisms based on bioecological traits appeared as efficient tools for the evaluation of catchment disturbances, at least for the benthic and the vegetation fauna.