The freshwater snail Theodoxus fluviatilis (Neritidae) is one of the most widely distributed gastropod species of the family Neritidae. The species is particularly sensitive to the quality of its environment, mainly due to its nutrition mode, which makes it a very good bioindicator of freshwater environments. Here, we examine the occurrence of this species in the Upper Rhone river by morphological observations and environmental DNA detection, in order to assess the impact of environmental changes on this particularly sensitive ecosystem. The Upper Rhone has been extremely altered by human activity. The main consequence of these changes has been the disappearance of species and the drying up of secondary streams (floodplain) connected to the Rhône. To restore the Rhône's biodiversity and hydraulic profile, an environmental and hydraulic restoration program was initiated, since the 1990s, on the Upper Rhône by the Compagnie National du Rhône (CNR). After restoration, Theodoxus fluviatilis was observed in large quantities in the wildlife surveys and was considered as a positive witness of changes introduced by restoration. Unfortunately, recently Theodoxus fluviatilis has disappeared from the sites where it was previously present in large quantities, possibly due to the effect of periodic emptying of Verbois dam that flushed the sediments down the river. Environmental DNA (eDNA) detection is a non‐invasive technique that can provide reliable information about a macrobial species occurrence based on intra- and extracellular material shed by an organism into the environment. Here, we developed a non-invasive quantitative PCR (qPCR) approach to detect Theodoxus fluviatilis in eDNA from water and sediment samples. First, we collected different individuals of Theodoxus fluviatilis from three different populations to obtain reference DNA sequences and create specific primers and probe for qPCR. After extensively testing the specificity and sensitivity of our method, we used this approach on thirty replicates from ten sites. We obtained positive eDNA detection for sites where the species was present in morphotaxonomic biodiversity surveys, and no detection at sites where the species was not found by morphological approach. The match between both approaches confirmed that the eDNA detection method provides a congruent presence/absence response, and that the future use of this method for quantitative assessment of Theodoxus fluviatilis in freshwater is promising.