This study provides the basis for implementing a continuous treatment system for wastewater containing a pesticide mixture formed by atrazine, iprodione, and chlorpyrifos. Two fungal strains (Verticilium sp. H5 and Metacordyceps sp. H12) isolated from a biomixture of a biopurification system were able to remove different pesticide concentrations (10 to 50 mg L−1) efficiently from the liquid medium; however, the half-life of the pesticides was reduced and characterized by a T1/2 of 5.4 to 9.2 d for atrazine, 3.7 to 5.8 d for iprodione, and 2.6 to 2.9 d for chlorpyrifos using the fungal consortium. The immobilization of the fungal consortium in alginate bead was effective, with the highest pesticide removal observed using an inoculum concentration of 30% wv−1. The packed-bed reactor with the immobilized fungal consortium, which was operated in the continuous mode at different flow rates (30, 60, and 90 mL h−1), required approximately 10 d to achieve removal efficiency (atrazine: 59%; iprodione: 96%; chlorpyrifos: ~85%). The bioreactor was sensitive to flow rate fluctuations but was able to recover performance quickly. The pesticide metabolites hydroxyatrazine, 3,5-dichloroaniline, and 3,5,6-trichloro-2-pyridinol were produced, and a slight accumulation of 3,5,6-trichloro-2-pyridinol was observed. Nevertheless, reactor removal efficiency was maintained until the study ended (60 d).