Oligotrophic areas harbour low macrofaunal abundance and patchy distribution. In these areas it is necessary to test the reliability of biological indicators, especially those based on taxonomic sufficiency where the level of identification is balanced against the need for ecological information and could affect the efficiency of bioindicators. The BOPA (benthic opportunistic polychaetes and amphipods) index was applied in five coastal areas subjected to different perturbations (aquaculture, harbour, brine, sewage, and thermal pollution) in the Canary archipelago, an oligotrophic area of the Atlantic Ocean. Significant differences in the BOPA index between impact and control sites were only found in the area affected by a harbour. Perturbations such as aquaculture, brine or sewage discharge produce only a weak response of the BOPA index, whereas no effects were observed at thermal pollution-impacted locations. The BOPA index should be used with caution to establish the ecological status of coastal water bodies in the Canary Islands, since it was only reliable in strongly impacted regions (enlargement harbour works), but did not respond clearly to other man-induced perturbations.