Negative impacts of human activities on stream ecosystems include the reduction/modification of the connectivity between surface water and groundwater and the contamination of these resources. Vertical hydrological exchanges principally occur through the coarse surface sediments and the hyporheic zone (porous matrix) and these compartments have the property to store pollutants. Such hydrological exchanges participate in the self-purification of the stream and infiltration of polluted surface water can lead to the contamination of groundwater. A complete environmental monitoring program should therefore include the assessment of the biological quality of the porous matrix and of the dynamics of vertical hydrological exchanges. The Functional trait (FTR) method based on the study of oligochaete communities in the coarse surface sediments and the hyporheic zone, allows simultaneous assessment of the effects of pollutants present in these compartments and the dynamics of vertical hydrological exchanges. Here, we applied the FTR method upstream and downstream of the effluents of three different wastewater treatment plants (WWTPs) whose discharges were significantly polluted, and for one of them (Oberglatt), before and after its upgrading. We could clearly observe negative effects of the effluents of each of these WWTPs on oligochaete communities and the Oberglatt WWTP upgrading resulted, compared to the state before the upgrading, in a significant reduction of the polluted sludge effect at the downstream site of the effluent. In addition, the method allowed us to identify several sites where the stream had a high capacity to self-purify (through exfiltration of groundwater) and other sites where groundwater was vulnerable to pollution by surface water.