Subsurface structures and especially the interactions between pores, roots and other organic matter elements have a strong impact on ecosystem functioning. Yet despite recent progress in the application of X-ray Computed Microtomography (µCT) to soil structure in agricultural science, applications to the more complex and heterogeneous substrates found in natural soils, specifically wetland soils, remain sparse. We apply X-ray µCT to a complex heterogenous soil and develop a robust segmentation method to quantify the pores, live roots and necromass. This approach significantly improves the detection of the organic matter elements, and gives us unprecedented detail and resolution in the segmentation of pores, live roots and necromass at a high spatial resolution (62.5 µm in this study). We identify several situations where pores and organic matter interact in the soil, including the disconnected air spaces (aerenchyma) that run within the Spartina stem and roots, tubular-shaped pores left behind by decaying roots, and lateral roots deploying within structural fragilities in the sediment. The capacity of X-ray µCT to distinguish the connected live root system from the necromass opens possibilities for applications to determine key wetland soil functions such as soil cohesivity, soil nutrient exchanges and soil carbon dynamics.