Glyphosate (G) is a broad-spectrum systemic organophosphate herbicide being widely used to control weeds in agricultural fields and urban areas. Its safety for both human health and aquatic biomes is a subject of wide debate. This study was aimed at evaluating the removal efficiency and ecotoxicity of G based herbicide (GBH) Klinik® (Nufarm, Austria) added to the raw municipal wastewater (WW) in a lab-scale model column system. The effect of oxide ceramics as a filtering medium (treatment „B”), as well as activated sludge and nutrients (treatment „C”) was compared with the control columns, which contained only WW (treatment „A”). After 72h treatment of WW spiked with 100 mg/L G, the lowest G concentration was detected in the treatment „B”, i.e., 79.4±0.6 mg/L. Treatments „A” and „C” resulted in the remaining G concentrations of 83.3±3.8 and 89.6±3.7 mg/l, respectively. The second addition of 100 mg/L G to the columns followed by 72h incubation also showed the advantage of oxide ceramics. Most probably, this effect could be explained by coupled sorption and biodegradation processes. Experiments were accompanied by microbiological (colony forming units; biological oxygen demand) and ecotoxicological (Daphtoxkit F magna, MicroBioTests) testing. The results indicated that WW-derived microorganisms resist the presence of GBH in the tested concentration range of G, i.e., up to 300 mg/L. As for Daphnia magna, the 24-h EC50 for the GBH Klinik® under standard conditions and in raw WW was found to be 22 mg/L and 6 mg/L G, respectively.