Native fauna of the tropical volcanic part of Guadeloupe is amphidromous: juveniles born in rivers but that grow in the sea need to migrate upstream to colonise their adult habitat in rivers. This migration is affected by any human-made obstacles placed in their way. Moreover, on volcanic tropical islands, streams are the main source of water catchment for the human population. This deeply affects river hydrology and characteristics. Both damming and water catchment potentially affect community diversity and species demography, but they may also alter the trophic ecology of the river fauna. Using stable isotopes and the stable isotope Bayesian ellipses approach in R (SIBER), this study aimed to assess the isotopic niche variability of riverine fauna of three persistent small rivers of Basse-Terre Island (Guadeloupe) affected by damming and water catchment. Using electrofishing, decapods and fishes (gobies) of three rivers were sampled upstream and downstream of dams. Our results demonstrated that the variability of the isotopic niches was extremely high between rivers but varied less between stations of the same river. Our results revealed complex and river-specific effects and a pattern merged with natural variability. Our two hypotheses (i.e., increase of resources upstream of dams and differential responses of trophic guilds to damming and water catchment) were only weakly supported and never in an unambiguous manner. Our study showed that it is necessary to consider the ‘noise’ generated by natural variability to observe and understand changes in the trophic ecology of associated fauna in relation to damming and water catchment.