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Low-impact, green infrastructure systems such as biofilters, particularly when amended with biochar, can help address chemical pollution conveyed via stormwater that is increasingly posing a threat to aquatic ecosystems and groundwater quality. Although removal of organic contaminants including pesticides by biochar-amended systems has been studied, the role of a biofouling layer on contaminant removal, biotransformation, and filter lifetime remains poorly understood. This study evaluated the removal of the pesticides atrazine, imidacloprid, and clothianidin in biologically active biochar-amended columns through complete exhaustion of contaminant removal capacity. The resultant data indicate that biological processes accounted for 20–36% of overall removal in the biochar-amended sand columns. In addition, a combined target and suspect screening approach using liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QToF-MS) was employed to evaluate the potential transformation of these three pesticides and release of the transformation products (TPs). All TPs detected in the effluent remained below 2.5% of their respective parent influent concentrations for the duration of the experiment. Furthermore, at a biochar application rate of 0.5 wt%, the presence of an active biofilm prolonged the filter lifetime by 1.8–2.3 times compared to a fouled but inactive filter, where removal was presumably dominated by adsorption only. Scenario modelling estimates showed that biochar-amended biofilters could last at least 17 years before exceeding aquatic life threshold values at biochar-application rates as low as 1 wt% (5 vol%) in a representative case study. Results of this study provide novel insight on pesticide TP formation in biochar-amended biofilters and estimation of filter lifetimes.