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The archaeological site of Biskupin (Poland) is a prehistoric settlement dating to the 8th century BC, situated on a marshy island. Excavations started in 1934 and a considerable number of wooden artifacts were found in the lake water. Unfortunately, during many years of archaeological excavations, wooden remains deposited in the trenches were exposed to degradation and underwent considerable decomposition. Among the main causes of wood degradation, fungi and bacteria were the most destructive ones. The chemical effects induced by fungi and bacteria on wood are not well-known or studied. Here we present the investigation of a set of pine wood samples (Pinus sylvestris) buried in the Biskupin site, with the aim of reproducing the burial conditions of the original archaeological wood. Two monitoring stations (wet peat and lake water) were chosen and the samples were then removed from these burial environments after four and ten years. After removal, the samples were exposed to laboratory-controlled attack by the brown rot fungus Coniophora puteana. The final aim was to evaluate the effects of fungal activity on the wood substrates with different degrees of natural degradation. The study is part of an experiment designed to evaluate the short-term effects of the in situ preservation strategy adopted for the Biskupin archaeological woods. Various techniques were used to assess the physical and chemical degradation of the wood. The morphological changes induced by the exposure to the burial environment and by the action of the fungi were investigated using scanning electron microscopy (SEM). The chemical state of the wood was evaluated by using infrared spectroscopy (FTIR), analytical pyrolysis coupled with gas chromatography and mass spectrometry (Py-GC/MS) and XRD spectroscopy. Fungal action caused the depletion of polysaccharides resulting in mass loss and the FTIR spectra of the wood samples highlighted that cellulose was more degraded with respect to hemicelluloses. This trend correlated with an increase in the relative abundance of furans, which are among the main pyrolysis products of polysaccharides. Fungal attack also induced oxidation of lignin and an increase in the crystallinity index of cellulose, which points towards a preferential metabolisation of amorphous cellulose. The overall results highlighted that the burial in these wet environments caused changes mostly in the hemicelluloses, whereas the fungal attack was mainly directed to cellulose degradation.