Urban freshwater ecosystems receive a wide array of organic pollutants through wastewater treatment plant (WWTP) discharges and agricultural runoff. Evaluating the fate and effects of antibiotics and pesticides can be a challenging task, especially the effects on freshwater vertebrates because of their abilities to metabolize and excrete these chemicals, and because of their high mobility and escape behavior when exposed to stressful environmental conditions. In the present study, 37 wild gudgeons (Gobio gobio) were caged for a period of up to 20 days, upstream and downstream of a WWTP effluent discharge in the Orge River (a tributary of the Seine River, France). The pesticides and antibiotics’ levels were weekly monitored in the fish muscles and compared to environmental contamination (water and sediments). Our results highlighted a slight impregnation of pesticides in the gudgeon muscles, at the downstream site, after 20 days of exposure. Concerning antibiotics, ofloxacin was the most detected compound in fish muscles (85% of occurrence) and ranged from undetectable to 8 ng.g‐1 dry weight. Antibiotic levels in fish muscle were not higher at the downstream site and did not increase with exposure duration, despite high levels in the water (up to 29 times greater than upstream). Potential ecotoxicological effects were also evaluated: body condition did not differ between the caging location and exposure time. Three oxidative status markers in the fish livers showed significant shifts after 14 days of caging. Our results suggest a high clearance rate of antibiotics and to a lesser extent, of pesticides in wild gudgeons, which could be explained by changes in xenobiotic metabolism with pollutant exposure.