In this paper, a diagnostic evaluation of the state of the art of archaeological waterlogged foundation piles in Riga Cathedral (1211 CE) was carried out. Microscopic, chemical and instrumental methods were applied to study the impact of deterioration of piles leading to the deformations of the Cathedral building. Severe biodeterioration by microorganisms in the majority of pile samples was determined. Chemical analyses showed an extensive depletion of hemicellulose and cellulose sugars while lignin seemed to be unaffected. Restricted degradation of hemicellulose sugars –arabinose and galactose – was characteristic of bacterial degradation of wood. FTIR spectroscopy proved itself as a quick and efficient method for determination of changes in wood components in foundation piles in comparison with chemical method. The increased ash content (up to 70%) in waterlogged wood consisted of deposited salts, oxides and other inorganic compounds. The X-ray diffraction method determined the main inorganic impurities, including calcite, quartz, sodium magnesium silicate and muscovite.