The evaluation of the impact of gradual environmental changes, such as the salinization of freshwaters, requires measures that are sensitive enough to detect the subtle changes that may be occurring within a population. Fluctuating asymmetry (FA) has been used widely to investigate questions regarding fitness and behavior, and to study the effects of environmental pollution. Asymmetries in the femur lengths of Calopteryx splendens (Odonata) larvae, and in the femur lengths, the tibia lengths and the pygopod widths of Hydropsyche exocellata and H. contubernalis (Trichoptera) larvae were studied at three sites along a salinity gradient of the Meurthe River (France). The difference in salinity between the sites (ranging from 0.21 to 2.60 g.L−1) was the only parameter varying to a degree significant enough to potentially affect damselfly or caddisfly development and their population densities. While no directional asymmetry or anti-symmetry was found, fluctuating asymmetry was observed for each species, each anatomic piece and for each site. Although C. splendens densities decreased along the salinity gradient, C. splendens FA did not differ significantly between traits and between sites. The same analysis on H. contubernalis showed that FA differed significantly between traits but not between sites in spite of a decrease of densities. H. exocellata FA differed significantly between traits and between sites but FA reached the lowest value for the intermediate salinity level. Finally, no relationships were observed between FA and the salinity gradient or between FA and the population density pattern observed for each species. Thus, according to our results, the FA of natural population of these insects seems to be a poor bioindicator of the salinity stress.