Oligochaetes are used in some cantons in Switzerland to assess the biological quality of watercourse and lake sediments. The oligochaete index of sediment bioindication (IOBS) allows to assess the quality of fine/sandy sediments of watercourses, while the Functional traits method (TRF) is dedicated to assess the quality of surficial coarse sediments and of the hyporheic zone. The TRF method also allows to know the dynamics of hydrological exchanges between surface water and groundwater. In the Geneva area, the IOBS index was applied in routine from 2008 to 2013 (92 samples) and the TRF method was tested in 2012 and 2013. The IOBS index proved to be a good bioindicator of chemical quality of the sediments. Metal toxicity thresholds in sediments were established and proposed. The implementation of the IOBS index in complement to the Swiss Biotic Index (IBCH) allowed to refine the ecological diagnostics. The TRF approach proved to be of great interest to simultaneously assess the biological quality of coarse habitats and of the vertical hydrological exchanges. The IOBS and TRF methods should be more integrated in the monitoring programs of watercourse quality. The current development of methods based on the identification of oligochaetes using genetic barcodes could allow to overcome the problems related to the morphological identification of species and a wider use of oligochaetes as bioindicators.