Combined effect of environmental change and management variability leads to reduced soil diversity in homogenous forest stands. On the other hand, forest soil diversity is maintained with rich tree species composition. In this study, focus has been put on deriving urgency to change forest tree species composition in order to increase soil diversity in biogeographic regions with uneven impact of environmental change. The relation of forest tree species and soil diversities was compared between the periods of dominant sulphur deposition (1985–1994) and the period of regional environmental change (2003–2012) in the Czech Republic (Central Europe; 78 866 km2; 115–1602 m n.m.). Forest tree species and soil diversities were assessed using linear regression, discrimination analysis and geographically weighted regression including residue analysis. The effect of spatial differences of acid deposition on soil properties, though, decreased, still dependencies between the diversity of bedrock, soils and forest tree species increased significantly. Only 12.9 % of forests in the territory of the CR have optimum tree species diversity. The total of 65.9 % of forest require highly or moderately urgent transformation. An increase in spatial dependencies between soil and tree species diversities confirms the importance of site differentiation in forest transformation.