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The performance of several indices of benthic functioning, based on the traits of estuarine macroinvertebrates, was tested in the lower Mondego estuary (Portugal), whose two arms exhibit different disturbance levels related to hydromorphology. The results showed that some indices responded clearly to this type of disturbance and others not so well. We argue that the communityweighted mean (CWM) trait values in combination with the newly developed SR-FRED index provided the best overall picture of how the benthic communities might have been affected by hydromorphological disturbance. This study also showed that certain indices should be used with caution when dealing with communities with few and dominant species, such as in estuarine environments.

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