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The paper presents the results of a study of the spatial organization of the solid phase of soils in relation to its functional characteristics. A comparison of the morphology and microstructure of the aggregates of sod-podzolic soil and chernozem showed that there is a relationship between the shape and size of the aggregates and the filtration coefficient. Electron microscopy of soil aggregates showed the differences in the microstructure of the studied soils, which is reflected in the degree of their resistance to water. The transformation of microstructure of constructozems was studied in a four-year-long (2012–2016) field experiment with the use of hydrological and electron microscopy methods. It is clearly correlated to the soil microstructure curves, especially in the organic horizons: Ap and peat. Our studies suggest that the soil architecture is a spatial organization of solid- phase soil components that form the structure of the pore space, which is hierarchical, functional differentiation, stability, development, and formed under the influence of biotic and abiotic environmental factors.