Benthic invertebrates are key components of food webs in particular by contributing to the transfer and transformation of allochtonous organic matter in river ecosystems. Many benthic invertebrates are known for their sensitivity to anthropogenic perturbations. One potential impact of perturbation is structural modifications in communities which can lead to functional changes. Trophic processes could be altered if community structure is deeply modified. Potential biological and ecological traits are a useful tool for studying functional characteristics of invertebrate communities. Focussing on two biological traits that describe the food and feeding habits of invertebrates, we quantified the specialization level of taxa and the intensity of trophic competition within benthic assemblages in selected mesohabitats of reference versus impacted sites. Several indices, including a new competition index, allow us to quantify the trophic specialization and trophic overlap of taxa and the within-community trophic competition intensity. The response of indices to four different perturbation types (i.e. acidification, organic pollution, habitat degradation and toxic pollution) was investigated for communities living in three mesohabitat types (cobbles, plants and litter) in 6 rivers of North-eastern France. Our results highlighted variable alteration in trophic structure depending on the perturbation and habitat types. The most drastic alteration was observed for invertebrate communities living in cobbles when subjected to organic pollution. Impacted communities were generally less specialized and exhibited lower trophic overlap than those living in reference conditions. The competition intensity was slightly affected by perturbation. Only organic pollution seemed to reduce competition intensity, but this trend was only significant for communities living in litter. This study suggests that perturbation, especially organic pollution, may alter trophic processes in rivers, through qualitative and quantitative modifications in trait profiles of taxa within benthic communities.