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Abstract Runoff from agricultural land often contains pesticide residues that can contaminate surface and groundwater, posing risks to ecosystems and human health. Therefore, there is a need to develop low-cost, effective, and environmentally friendly methods to mitigate this contamination directly at its source. This present study evaluates the efficiency of biofilters composed of biochar, vermiculite, and wood chips in removing pesticides from drainage waters in agricultural settings. A field-scale experimental setup was established using three different substrate configurations, including a vegetated mixture of sorbents with alder seedlings. Five commonly used pesticides (glyphosate, diflufenican, flufenacet, pyridate, and tebuconazole) were tested in exposure experiments simulating runoff events. Results showed that biofilters containing the planted mixture achieved the highest removal efficiencies, with glyphosate removal reaching up to 99.98%. Diflufenican and flufenacet were also effectively reduced, with the lowest removal still exceeding 96%. Pyridate was not detected after filtration, but its metabolite pyridafol was present in all setups, with the planted biofilter showing the lowest response. Tebuconazole demonstrated a significant reduction in vegetated substrates, likely due to root uptake and rhizosphere microbial degradation. The study confirms that combining natural sorbents with vegetation enhances pesticide retention through synergistic effects such as increased sorption and biological activity. This approach offers a low-cost, sustainable alternative to conventional water treatment technologies and may serve as a valuable tool for mitigating pesticide pollution in small agricultural watershed meeting goals of SDG 6 on Clean Water and Sanitation. Graphical Abstract