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The Kyoto-protocol permits the accounting of changes in forest carbon stocks due to forestry. Therefore, forest owners are interested in a reproducible quantification of carbon stocks at the level of forest management units and the impact of management to these stocks or their changes. We calculated the carbon stocks in tree biomass and the organic layer including their uncertainties for several forest management units (Tharandt forest, Eastern Germany, 5,500 ha) spatially explicit at the scale of individual stands by using standard forest data sources. Additionally, soil carbon stocks along a catena were quantified. Finally, carbon stocks of spruce and beech dominated stands were compared and effects of thinning intensity and site conditions were assessed. We combined forest inventory and data of site conditions by using the spatial unions of the shapes (i.e., polygons) in the stand map and the site map. Area weighted means of carbon (C) stocks reached 10.0 kg/m² in tree biomass, 3.0 kg/m² in the organic layer and 7.3 kg/m² in mineral soil. Spatially explicit error propagation yielded a precision of the relative error of carbon stocks at the total studied area of 1% for tree biomass, 45% for the organic layer, and 20% for mineral soil. Mature beech dominated stands at the Tharandt forest had higher tree biomass carbon stocks (13.4 kg/m²) and lower organic layer carbon stocks (1.8 kg/m²) compared to stands dominated by spruce (11.6, 3.0 kg/m²). The difference of tree biomass stocks was mainly due to differences in thinning intensity. The additional effect of site conditions on tree carbon stocks was very small. We conclude that the spatially explicit combination of stand scale inventory data with data on site conditions is suited to quantify carbon stocks in tree biomass and organic layer at operational scale. [ABSTRACT FROM AUTHOR]