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The primary objective of this study was to develop a reliable method for isolating and characterizing flow domains in a large undisturbed soil column using a CAT scanner. CAT scanning offers tremendous potential for non-destructive quantification of tracer volume concentration inside soil columns during breakthrough experiments. This approach allows for real-time examination of flow mechanisms through soil macropores at various depths along the length of soil columns. With the knowledge of the macropore structure and the spatial distribution of the solute, breakthrough in the macropore and matrix flow domains was evaluated. Flow in the matrix domain suggested that part of the matrix contains small pores that are connected to macropore networks. These pores contribute to a rapid tracer build up in the matrix domain. They were identified as mesopores. This suggests that the matrix domain should be sub-divided into two regions: the mesopores and the micropores.