During 2008 -- 2011 the effect of different agronomy practices on changes in topsoil and subsoil macrostructure was studied. Macrostructure refers to the ability of soil aggregates to resist dispersion. Three soil tillage treatments were established (conventional tillage with plowing; deep loosening to the depth 0.35-0.40 m; minimum tillage with shallow loosening to the depth 0.15 m). Three localities, three different crop growing regions in the different climatic conditions were studied (Unčovice -- Luvi-haplic Chernozem -- located in a sugar-beet growing region, Hrušovany-nad-Jevišovkou -- Haplic Chernozem -- located in a maize growing region and Lesonice -- Gleyic Luvisol -- located in a potato growing region). Crop rotation systems were as follows: rape, winter wheat, maize, winter or spring wheat, and spring barley. The best water stability of aggregates was found in the locality Hrušovany nad Jevišovkou. The worst water stability was found in the locality Lesonice. Results of water stability of aggregates corresponded mainly with the soil conditions in localities. In localities Hrušovany nad Jevišovkou and Lesonice, a significant positive impact of non-inversion variants was demonstrated. The best values of water stability values were found in the plowed variant in the locality Unčovice. These findings were not statistically significant. An effect of soil sampling period (spring, autumn) on the water stability of soil aggregates was observed as well. Obtained results helped us to suggest the evaluation scale of soil structure quality according to percentages of water stability of soil aggregates. At the same time it was also found out that both minimum tillage and deep soil loosening had a positive effect on crop yields (maize and winter wheat).