The intensification of agriculture has drastically modified the structure of rural landscapes, changing field size, destructinghedgerow networks, and increasing nutrients and fine sediments fluxes to rivers. To evaluate the effects of these disturbances atthe catchment scale, we studied the surface and interstitial water chemistry and the invertebrate assemblages in three differenthabitats: 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 andagricultural streams lie in changes in water chemistry, in habitat quality, and in the composition of the assemblages with littlereduction 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 ifwater 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 theriver) profoundly affected the system with drastic modifications of in-stream habitat quality and invertebrate assemblagecomposition. The effects of these disturbances differed according to the habitat considered, with increasing differences betweenassemblages from the interstitial, to the benthic, and to the vegetation habitats. Finally, groups of organisms based on bioecologicaltraits appeared as efficient tools for the evaluation of catchment disturbances, at least for the benthic and thevegetation fauna.