Efforts to enhance carbon storage in forest ecosystems through policy and management decisions rely on accurate forest biomass assessments. However, most forest inventories consider tree mortality the only form of aboveground biomass loss, overlooking other important factors, such as wood decay in living trees. In this study, using linear mixed-effects models, we delve into the sustainability of mature and over-mature deciduous forests in Latvia by conducting a comprehensive analysis of stem rot severity, identifying species for which the impact of stem rot on their carbon stock reduction was most significant. The analysis focused on determining the proportion of discolored wood, decomposed wood, and hollow spaces within the stems of 190 living deciduous trees commonly found in hemiboreal forests. The study reveals a greater extent of stem rot and more extensive decay in Populus tremula trees than in Betula spp., Alnus glutinosa, and Alnus incana. It emphasizes the influence of tree species, age, and diameter at breast height on stem rot proportions. The stump rot area significantly predicts the amount of decomposed and discolored wood within the stem. The study provides valuable insights for sustainable forestry practices and highlights challenges in estimating stem rot severity, emphasizing the need for comprehensive diagnostic methods.