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A survey was undertaken from April to June 1991 in seven sites of the Rhone River and the Ain River, southeastern France. A variety of physical and chemical factors were measured in an attempt to assess the importance of each in determining the distribution of species and the community structures at the surface/aquifer interaction zone. Metal (zinc and copper) impact was more precisely considered. Two investigation methods (multivariate statistical community analysis and community parameters such as abundance, richness, diversity indices) revealed that the structures of the surface and interstitial communities were partly related to some of the chemical factors and to variations in metal concentrations in the water or in the sediments. Variables such as magnesium, sulfate, potassium, oxygen, and metal contents appeared to be discriminant factors which could be associated with specific faunistic assemblages. Moreover, sites contaminated by zinc or copper generally had a low number of individuals and low number of taxa. Taxonomic groups were differently affected by metals. However, the potential use of epigean and especially hypogean invertebrate species in biomonitoring trace metal contamination at the river/aquifer interaction zone is as yet premature.