Weed control in winter wheat crops is an important issue. There is a risk of increasing populations of certain weed species that are resistant to some of herbicides used for winter wheat crops. This could be controlled by a combination of agronomic, mechanical, chemical, and biological methods. After introducing winter wheat into the rotation and improving tillage, the weediness of regular black soils with perennial root and emerged weeds were significantly reduced. The formation of nodal and rudimentary roots had a significant effect on the productivity of winter wheat under different soil moisture conditions. The highest yield of winter wheat was obtained when sown at the optimum time, with higher stem density and ear productivity due to better grain fullness. We studied what effects did the tillage methods have on the aggregate state of the soil in relation to weed development in winter wheat crops, finding that the structural and aggregate composition of the soil played an important role in winter wheat crops, influencing both the development of the crop root system and the water-physical balance of the chernozem, as well as naturally influencing the course of erosion processes in the experimental plots, and having a universal dynamic in terms of adaptation of aggregation and disaggregation processes. Prolonged mechanical stress on soil can cause destruction of its structure. For instance, continuous ploughing or moldboardless tillage with little or no manure application may permanently reduce soil fertility by increasing humus mineralisation. Subsequently, these factors may cause a significant decline in the soil's structural and aggregate composition, resulting in larger amounts of dusty particles smaller than 0.25 mm and cloddy particles larger than 10–12 mm. The soil's structural condition before sowing winter wheat in early September, on average for 2011–2016, indicates increased dispersion of the tilth layer (0–10 cm) in the experimental variants where shallow disc tillage of 10–12 cm was applied. Increase in the number of clods larger than 10 mm in the areas where moldboardless tillage had been applied can be attributed to significant soil drainage. The soil's aggregate state was rated as good, with 8.7% in the 0–10 cm soil layer and 1.7% of clods > 10 mm in the 0–30 cm layer. In 2014–2016, it was rated as satisfactory, with 7.4% and 9.8% of clods > 10 mm, respectively. Shallow disc cultivation resulted in slightly worse indicators: 6.6% and 8.3% of clods > 10 mm in soil layer 0–10 cm and 0–30 cm, respectively, in 2011–2013; and 7.2% and 6.9% of clods > 10 mm, respectively, in 2014–2016. In general, the parameters of optimal structural condition were positive. The tillage method used had a considerable effect on weed growth and development, particularly for those with a root and rhizome structure. It also affected the prevalence and development of pests and diseases in winter wheat. Agrotechnical methods of weed control do not guarantee complete destruction of weeds. Mechanical moldboardless tillage to the depth of 14–16 cm and disc tillage to the depth of 10–12 cm left the fields with 4.1 to 8.8 annual weeds per square meter and 1.3 to 3.3 specimens of harmful root weeds such as Convolvulus arvensis, Lactuca tatarica and Cirsium arvense. Mechanical moldboardless tillage to the depth of 14–16 cm and disc tillage to the depth of 10–12 cm left the fields with 4.1 to 8.8 annual weeds per square meter and 1.3 to 3.3 specimens of harmful root weeds such as Convolvulus arvensis, Lactuca tatarica and Cirsium arvense. Post-harvest residues (4–5 t/ha) can provide almost complete protection against weeds by covering the soil surface. However, pests and diseases may spread more easily due to preservation of fungal spores on the surface of plant residues and preservation of pest larvae in the straw and soil. The distribution of weed seeds in the soil was altered when the rotational tillage of common chernozems in winter wheat cultivation technology had been replaced with energy–saving minimum tillage (shallow flat-cutting disc tillage). This resulted in the concentration of most of the weed seeds (85–90%) in the upper soil layer (0–10 cm).