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In West Africa different insecticides had been applied in selected river areas for the reduction of the blackfly populations vectors of Onchocerca volvulus, a parasite causing blindness. To evaluate the possible long term effects of the larvicides on the non target fauna an aquatic monitoring programme has been up from the initial phase of the project. Addressing the attention to the invertebrates data collected in four countries during a maximum period ranging from 1977 to 1996, this paper shows and discusses the data analysis strategy for the measure and interpretation of the biological variation. In particular the application of quantitative ecological analysis methods: Principal Component Analysis, rank abundance models and the community diversity indexes, is critically discussed and comments are given to the ecological interpretation of the results.