Wastewater discharge is one of the main sources of micropollutants within the aquatic environment. To reduce the risks for the aquatic environment, the reduction of the chemical load of wastewater treatment plant effluent is critical. Based on this need, additional treatment methods, such as ozonation, are currently being tested in several wastewater treatment plants (WWTPs). In the present study, effects were investigated using in situ feeding experiments with Gammarus pulex and body burden analyses of frequently detected micropollutants which used a Quick Easy Cheap Effective Rugged and Safe (QuEChERS) multi-residue method to quantify internal concentrations in collected gammarids. Information obtained from these experiments complemented data from the chemical analysis of water samples and bioassays, which predominantly cover hydrophilic substances. When comparing up-and downstream feeding rates of Gammarus pulex for seven days, relative to the WWTPs, no significant acute effects were detected, although a slight trend of increased feeding rate downstream of the WWTP Aachen-Soers was observed. The chemical load released by the WWTP or at other points, or by diffuse sources, might be too low to lead to clear acute effects on G. pulex. However, some compounds found in wastewater are able to alter the microbial community on its leaves, leading to an increase in the feeding rate of G. pulex. Chemical analysis of internal concentrations of pollutants in the tissues of collected gammarids suggests a potential risk for chronic effects with the chemicals imidacloprid, thiacloprid, carbendazim, and 1H-benzotriazole when exceeding the critical toxic unit value of −3. This study has demonstrated that a combination of acute testing and measurement of the internal concentration of micropollutants that might lead to chronic effects is an efficient tool for investigating river systems, assuming all relevant factors (e.g., species or season) are taken into account.