Ecological quality assessment of small estuaries from the Portuguese coast based on benthic macroinvertebrate assemblages indices

► We studied five small estuaries with different levels of anthropogenic pressures. ► Benthic macroinvertebrates indices were used to differentiate ecological status. ► The correspondence of indices results to anthropogenic pressures was examined. ► The analysis of indices metrics was more informative than indices results. ► Indicators were unable to distinguish natural from anthropogenic perturbations.