We studied the environmental effects of the mining activity of Troya Mine on the fluvial ecosystem, in the Basque Country, Spain, from 1993 to 1995. The multivariate analysis of the physicochemical conditions shows that the main abiotic factors of variation are: (i) in the water column, a significant increase in the content of heavy metals and conductivity, and (ii) an intense accumulation of heavy metals in the bottom sediments. We studied the effects of these factors on density, richness, dominance, similarity coefficient and composition of the benthic macroinvertebrate community (BMI).We observed a de-structuring of the community. Richness decreases (from 25 to 11 different number of families), but it does not suitably value the impact. Density oscillates radically (255–1548 individuals m⁻²) and reflects changes occurred in sediments. Dominance, which oscillates from 0 to 1, increase from 0.16 upstream from the mine, to 0.42 downstream, fundamentally due to oscillations of Chironomidae, Tubificidae, Baetidae and Simuliidae. The similarity coefficient indicates the physicochemical variations both in the sediment and in the water column; this index is therefore suitable for the follow-up of the evolution of the disturbance studied. The families sensitive to disturbance in the water column are: Ephemeridae, Athericidae, Sericostomatidae, Leptophlebiidae, Baetidae, Gammaridae, Perlidae, Heptageniidae, and Leptoceridae; the tolerant ones are: Coenagrionidae, Hydrobiidae, Lumbricidae, and Polycentropodidae.With regard to the metal content in sediments, the sensitive families are: Gammaridae, Ephemeridae and Ceratopogonidae; the tolerant ones are: Simuliidae, Culicidae, Hydrophilidae, Dolichopodidae, Chironomidae, Psychodidae, Tipulidae, and Chrysomelidae.We thus synthesized the complexity inherent to this type of pollution, in which large amounts of variables are normally involved.