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Constructed Technosols are frequently used to create the biofilter layer of blue-green infrastructure elements when the local soil does not possess the necessary properties. However, the long-term functioning of the biofilter is not entirely understood. The aim of this study is to elucidate changes in the structure of a constructed Technosol based biofilter of a bioretention cell (BC) by means of x-ray tomography and additional physical characterization during the first years after installation under two different water regimes. Two identical experimental BCs were studied to investigate structural changes in biofilter. The BCs exhibited different water regimes. BC1 collected naturally occurring rain concentrated from the nearby roof, while BC2 lacked a regular inflow of water except for several irrigation events and exhibited drier conditions overall. Biofilter was constructed using a mixture of 50% sand, 30% compost, and 20% topsoil. Undistributed soil samples were collected from the biofilter at 7, 12, 18, 23, and 31 months after BC installation. The changes in the soil pore system geometry were assessed by analyzing morphological parameters derived from X-ray computed microtomography images (μCT) and additional physical parameters. The μCT images were analyzed using the SoilJ software package. In both BCs, soil consolidation accompanied by a significant reduction in macroporosity and pore connectivity, occurred between months 7 and 18 in BC1 and between months 7 and 12 in BC2. Macroporosity then gradually increased in BC1 between months 18 and 31. During the same period, in the drier soil of BC2, macroporosity and pore connectivity decreased. In BC1, the water field capacity increased between months 7 and 18, but then returned to its initial values by month 31. The μCT proved to be suitable for assessing the structural changes of constructed Technosol. Significant differences in soil structure development were observed in BC, depending on the water regime. These differences were particularly evident in the development of field capacity, total porosity, and macroporosity.