X-ray microscopy iscapable of imaging particles in the colloidal size range directly in their aqueousenvironment with high spatial resolution.It is possible to combine this with high spectralresolution for spectromicroscopic studies.Two types of microscopes are common in X-raymicroscopy,the transmission X-ray microscope and the scanning transmission X-raymicroscope,whose setup is shown in this paper.While an X-ray microscope quickly takes highresolution images from an object,a scanning X-ray microscope as an analytical instrumentis suited for spectromicroscopy.As an example for visualization of morphology,clay andsoil samples have been imaged with a transmission X-ray microscope.Images from acryotomography experiment based on X-ray microscopy images to obtain information about the3D structure of microhabitats formed by bacteria and other soil colloids are shown.Theanalysis of a stack of images taken with a scanning transmission X-ray microscope to bringtogether morphology and chemistry within a soil sample is given.