Rivers are one of the most commonly transformed aquatic ecosystems. Most papers present significantly negative effects of activities such as dredging or channel regulation on the ecological status of rivers. The purpose of this work was to compare the response of various groups of invertebrates (Mollusca, Hydrachnidia, Odonata, Heteroptera, Coleoptera and Trichoptera) to an intervention involving dredging in conjunction with the removal of riparian vegetation. Habitat diversity increased after the dredging, and more individuals and species were caught than before the dredging. The increase in habitat diversity after the dredging translated into an increase in the species diversity of most investigated groups. Individual groups of invertebrates showed varied responses to the dredging, depending on the role of the terrestrial phase in their life cycle: the greater the role of the terrestrial phase in the life cycle, the more the group was affected by changes in the terrestrial environment following the intervention. In consequence, the intervention had the greatest negative impact on insects, and among these, on adult Odonata. The following conclusions can be drawn: (1) Dredging can benefit a previously anthropogenically transformed river ecosystem by increasing habitat diversity; (2) Odonata are particularly useful for assessing the impact of this type of intervention on invertebrate communities. They can be considered good indicators of habitat disturbances in both aquatic and terrestrial ecosystems.