Three-dimensional imaging and image processing has become an important part for investigations of fluid distribution and flow in porous media. We describe two methods of computed tomography with different characteristics, namely X-ray- and neutron-based. We give an overview of image processing sequences and their methods. We investigated image enhancement with a focus on filters using partial differential equations, classification and structure identification that we used to prepare our images for quantitative evaluations. These methods are demonstrated on a partially saturated sand sample. Finally, we show an application with soil aggregates where investigations using synchrotron X-rays and thermal neutrons have led to new insights and refined fluid distribution and flow models.