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Fertiliser and pesticide application can cause extensive environmental damage. We use the water quality footprint to express nitrogen, phosphorus and glyphosate emissions from agriculture in volumes of water needed to virtually dilute pollution and apply the approach to agricultural imports for the German bioeconomy in 1995 and 2020. In total, the virtual German water quality footprint corresponds to 90 times the volume of Lake Constance. If water pollution had to be eliminated by dilution in export countries supplying Germany, volumes would be by a median of 300 times higher than the associated irrigation volumes there and could exceed natural water availability. Important and growing hotspots of clean water scarcity are China, Spain and India. The impact of German agricultural supply chains needs to be monitored with regard to the sustainability of national consumption and to the effectiveness of increasing fertiliser and pesticide use, especially in African, Asian and Pacific countries.