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During four different time periods artificial substrates (polyuréthane blocs) were used to sample ciliates in a river receiving different kinds of pollution. 46 species of ciliates were found, belonging to 40 genera. Their distribution and abundance varied greatly both along the river and with time. The saprobic index method was used to localise sources of organic inputs and follow their change with time. Community structures were analysed through specific diversities and rank-frequency diagrams. This allowed the discovery of toxic chemical inputs and their relative intensities. A parallel study of chemical and physical-chemical pollution indicators of the water confirmed the biological results.