X-ray tomography has proven to be an effective tool for three-dimensional analysis of particle deposition in deep bed filtration. A major challenge in terms of quantitative data evaluation of such tomographic images is the implementation of a reliable image decomposition method in quantifying the various materials in a filter bed which has been flooded with water and contains particle depositions. Therefore, a multistage method, based on basic image processing operations, has been developed to decompose grayscale images of multiphase systems into sets of concentrations for each phase. In that regard, the quantification of strong absorbing particles below the resolution limit is of particular interest in order to enable the detection of particle deposition sites at the beginning of a filtration process. The method was tested on three model samples, consisting of glass, molybdenum particles and polyurethane, as a substitute for water, with entrapped air. It could be shown that the particle concentration can be determined for all samples with a maximum error of 14.5 %.