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Sustainable horticulture depends on the integrity of soil functions, which directly depend on soil architecture affecting aggregation, root growth, as well as liquid and gas permeability. We hypothesised that changes in soil architecture resulting from feedback mechanisms between management, soil organic carbon contents (SOC), biota and vegetation can be captured with X-ray computed tomography (CT), and that these affect the soil filtering function, which thus, can be manipulated through orchard management. We compared the transport of copper, a widely used fungicide, through intact soil cores from vine rows of kiwifruit orchards under organic and integrated management. We first derived 3D-macropore characteristics from CT-images, followed by leaching a pulse of copper and a tracer through the same cores. The organic orchard soil had a significantly higher SOC content than the integrated orchard soil, and this was positively correlated with total porosity. Macropores (>92 mu m) were larger with a higher connectivity, but significantly fewer in the organic than the integrated orchard soil. This resulted in a lower macroporosity and a better copper filtering capacity of the organic than the integrated orchard soil. Copper distribution was reasonably predicted when combining SOC contents, pH and macropore characteristics. Significant relationships between soil parameters and indicators of the strength of preferential flow verified that CT-derived macropore characteristics can be used to predict functional solute transport parameters. The relevance of our results and relationships observed between macropore characteristics, functional indicators of preferential flow and the fate of copper needs verification with samples representing more soils and sites.