Collecting quantitative data on insect species occurrence and abundance is a major concern to document population trends. This is especially the case to assess the conservation status of species listed in the European Habitats Directive and to assess the efficiency of mitigation measures with a view to achieve the “no net loss of biodiversity” goal for protected species. However, at present, populations of riverine dragonflies listed in the Habitats Directive and protected under French national law are poorly quantified and monitored. Exuviae collection could be used for such monitoring but a standardised protocol is lacking. We here proposed and tested such a protocol to monitor riverine dragonfly populations through exhaustive exuviae collection along river bank transects. To define the optimal transect size and number of visits, ninety-eight 100 m-long transects divided into 10 m-long plots were monitored on three rivers in southern France. Each transect was visited three times over the emergence period. In the course of each visit, all the exuviae along transects were collected and identified. From our results, we recommend collecting exuviae along 100 m of river bank in the course of two visits in order to both maximise the species detection and minimise the monitoring cost.