Chemical, physical, and biological decay may partially or totally hide the historical and technological information carried by waterlogged wood. Investigation of the above-mentioned decay processes is essential to assess the wood preservation state, and it is important to find new methods for the consolidation and safeguarding of wooden archaeological heritage. A conventional method for assessing the wood preservation state is light microscopy. However, the method requires sample slicing, which is destructive and challenging when dealing with fragile and spongy submerged remains of heritage wood. To this end, a promising alternative non-destructive technique is proton nuclear magnetic resonance (1H-NMR) which considers wood as a porous system. This work aimed to perform a comprehensive analysis of structures, porosity, water distribution, decay, and possible structural inclusions of three archaeological waterlogged wood fragments of the Roman age using NMR relaxometry, micro-imaging (μ-MRI), NMR diffusometry, and NMR cryoporometry. The results were compared with a similar analysis of the three contemporary wood samples of the same species. The multimodal approach presented in this study allowed us to cover all the dimensional scales of wood, from nanometers to sub-millimeters, and reconstruct the alteration of the entire archaeological wood fragment caused by degradation.