Developing a holistic understanding of the biological deterioration of wooden material by fungi in the laboratory and outdoor conditions requires the development of new assessment procedures and tools that allow describing the process with maximum precision and accuracy. Environmental biodeterioration is a complex process including a combination of physical, chemical and biological changes, with many uncertainties limiting the predictability and effectiveness of selected preservatives after laboratory tests. Therefore, in the current thesis, the investigation of the effectiveness of selected wood process parameters and protection systems against fungal growth and evaluation of the applicability of near-infrared spectroscopy for wooden surfaces assessment under fungal attack were accomplished.  The mould attack on copper impregnated Scots pine sapwood regulated to a greater extent by planing depth than by the infection method. Air-borne contaminants can heavily occupy the unplaned surfaces, but the extent of such occupation could be reduced with planing and impregnation solutions. Despite the vulnerability of the differently planed and copper-impregnated wood towards mould fungi, mass loss of that wood degraded by white-rot Trametes versicolor was less than 5%. The distribution, quantity, and nature of lipophilic substances beneath the surface in the air- and kiln-dried Scots pine sapwood boards significantly influenced mould fungi attack. It was found that the concentration of total extractives was significantly higher in kiln-dried than in air-dried samples and was higher close to the surface than in the layers beneath. During kiln-drying, a migration front is created at a depth of 0.25 mm with a thickness of about 0.5 mm. The evidence from the previous study is committed to understanding the influence of extractives and other migrating compounds on the unplanned surface and, consequently, on mould growth on that surface of Scots pine sapwood subjected to air and kiln drying. Therefore, a multivariate regression model was developed.  The thermal modification at different temperatures of exotic African wood influenced the chemistry. Iroko wood demonstrated stabilisation of pH and different patterns of chemical changes compared to padouk.  The open process of wood treatment like heating-and-cooling (i.e. fully soaking heated wood in cold liquor allowing the liquor to penetrate wood partially) can improve wood performance by developing a protective layer beneath the surface on heat-induced curing. However, the applied methacrylic resin demonstrated effectiveness during laboratory testing for biodeterioration but did not perform efficiently during outdoor tests.  The test of available commercially of generally recognised as safe (GRAS) compounds and biocidal treatment in laboratory conditions revealed a moderate inhibition effect on protection against biodeterioration.  Hyperspectral imaging in the NIR region could be applied to classify thermally modified wood but not for air/kiln-dried Scots pine wood. The use of a portable microNIR spectrometer efficiently demonstrated the separation of no mould and mould specimens in laboratory tests of Scots pine and allowed classifying boards treated with commercial biocides after outdoor weathering.