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Growing global demand of water use, and regional changes in precipitation in many regions, has resulted in increasing long-term irrigation of agricultural soils with post-treatment waste water. Overlaying this trend with the rising use of pharmaceuticals has created a new pathway for these pollutants, including biologically active compounds such as antibiotics, to enter the soil environment. We present results from a new interdisciplinary study of the response of an agroecosystem which was repeatedly contaminated with a typical combination of antibiotics at a representative concentration found in waste water effluent. Results from this experimental manipulation, show the impact of different concentrations of antibiotics in the soil and the unexpected repercussions throughout the agroecosystem. This includes effects on soil microbial communities, microbial function (anti-microbial resistance), abiotic soil condition, antibiotic persistence in the soil, ecosystem function (greenhouse gas exchange) and the effect on the arable crop itself. Implications of this study are relevant to fully understanding the impact of this land management technique on the sustainability of food production.This study was funded through the UK’s N8AgriFood Programme.