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The agroecological transition offer opportunities to reduce agriculture's environmental impacts by reducing reliance on synthetic fertilisers and pesticides. Crop diversification, in both time and space, is a key strategy including extended crop rotations, intercropping, and cover crops. Yet, relationships between reduced input use and associated environmental impacts remain insufficiently quantified. We assessed the environmental performance of six innovative low-input cropping systems that used cover crops, cultivar mixture and intercropping in term of nitrogen fertiliser and pesticide use, as well as nitrate and pesticide losses. From 2010 to 2016, cropping systems were monitored for input use and drainage water was collected with tension plate lysimeters at 1 m depth. Nitrate and up to 44 pesticide compounds were analysed annually. Nitrogen fertiliser application varied across systems, with more diversified systems applying less thanks to legumes. Pesticide use remained similar among systems but reduced by over 50% compared to conventional rates. Cover crops played a key role in reducing pollution. Nitrate leaching reduced by 42–56% in systems with cover crops. More originally, pesticide leaching decreased by 53–82% for these systems with S-metolachlor representing more than 50% of the quantity of pesticide losses. These results demonstrate that diversifying cropping systems, particularly through cover cropping, can reduce agriculture's environmental footprint greatly. When combined with reducing input use, such strategies provide a promising pathway towards more sustainable and resilient farming systems, with clear benefits for water quality and agroecosystem functioning. • Six low-input diversified arable cropping systems were tested for six years. • Nitrate and pesticide leaching were collected over the six years of monitoring. • Cover crops cut nitrate leaching by 42–56% under field conditions. • First evidence that cover crops reduce pesticide leaching by 53–82%. • S-metolachlor loss is the main driver of the pesticide leaching pattern observed.