In this work, a sand filtration-activated carbon adsorption system was evaluated to remove the fungicide content of a biologically treated effluent. The purification process was mainly carried out in the activated carbon column, while sand filtration slightly contributed to the improvement of the pollutant parameters. The tertiary treatment system, which operated under the batch mode for 25 bed volumes, resulted in total and soluble COD removal efficiencies of 76.5 ± 1.5% and 88.2 ± 1.3%, respectively, detecting total COD concentrations below 50 mg/L in the permeate of the activated carbon column. A significant pH increase and a respective electrical conductivity (EC) decrease also occurred after activated carbon adsorption. The total and ammonium nitrogen significantly decreased, with determined concentrations of 2.44 ± 0.02 mg/L and 0.93 ± 0.19 mg/L, respectively, in the activated carbon permeate. Despite that, the initial imazalil concentration was greater than that of the fludioxonil in the biologically treated effluent (i.e., 41.26 ± 0.04 mg/L versus 7.35 ± 0.43 mg/L, respectively). The imazalil was completely removed after activated carbon adsorption, while a residual concentration of fludioxonil was detected. Activated carbon treatment significantly detoxified the biologically treated fungicide-containing effluent, increasing the germination index by 47% in the undiluted wastewater or by 68% after 1:1 v/v dilution.