Context: 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. Objective: 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. Methods: 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. Results and Conclusions: 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. Significance: 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.