Agricultural runoff often contains persistent halogenated herbicide compounds like 2-(ethylamino)-4-(isopropylamino)-6-(methylthio)-s-triazine (ametryn) and 3,6-dichloro-2-methoxybenzoic acid (dicamba). These can enter the food chain through drinking water, causing serious effects for people and the environment. A sequential anaerobic reactor followed by an aerobic reactor was operated and investigated for herbicide removal efficiency at constant, three-day, hydraulic retention time (HRT) and organic loading rate (OLR) of 0.2025 kg-COD/m3/d. The effect of the herbicides on anaerobic bacteria was evaluated based on total biogas production and bacterial activity, which indicated that there was no inhibition on the acclimated biomass. The sequential reactor pair removed 72% of ametryn and 78% dicamba, with COD removal efficiencies of 86% and 85% respectively. The different high-performance liquid chromatography (HPLC) peaks indicate that the compounds are biotransformed and this was confirmed by gas chromatograph high resolution mass spectrometry (GC-HRMS).