AbstractRelationships between invertebrates, substrate characteristics and trophic factors were investigated, with special emphasis on the hyporheic habitat, in order to characterize the functioning of different running waters ecosystems.Three contrasting study sites were chosen in catchments exhibiting different features: (1) a meandering reach of the Loire River in its alluvial floodplain, upstream of the ‘Bec d'Allier’; (2) a reach of the Galaure with a fairly developed riparian corridor, a small sinuous foothill river; and (3) a braided reach of the Drac, an alpine torrential stream.Each site was sampled once using the freezing‐core technique with previous electro‐positioning of the invertebrates. In each site, four 60 cm cores were extracted, each one from different morphodynamic units.In the Loire and Galaure rivers, most invertebrates are found in the first 15 cm of the sediment, with the exception of some particular taxa or morphodynamic units (riffle head). Conversely, in the Drac lotic units, maximum density of invertebrates occurs between 15 and 30 cm and more than 75 per cent of all organisms are found at a depth>15 cm. The vertical distribution of organisms does not follow a uniform pattern in different streams.In the substrate, the vertical distribution of macroinvertebrates is very closely related to porosity in contrast with trophic parameters that always decrease with depth. The porosity is negatively correlated with the percentage of sand in the sediment and seems to be important in determining the vertical distribution of fauna, and should be integrated in a functional typology of running waters.The trophic parameters and the structure of invertebrate community with its dominant feeding groups allow discrimination of the differen