In recent years, there has been an increasing interest around agricultural science and practice in conservation tillage systems that are compatible with sustainable agriculture. The aim of this study was to assess the qualitative and quantitative changes in weed flora and soil seed bank under reduced tillage and no-till (direct sowing) in comparison with traditional ploughing. In the crop rotation: pea/rape—winter wheat—winter wheat the number and dry weight of weeds increased with the simplification of tillage. The seed bank was the largest under direct sowing and about three times smaller in traditional ploughing. Under direct sowing, most weed seeds were accumulated in the top soil layer 0–5 cm, while in the ploughing system most weed seeds occurred in deeper layers: 5–10 and 10–20 cm. In the reduced and no-till systems, a greater percentage of perennial and invasive species, such as Conyza canadensis L., was observed. The results show that it is possible to maintain weed infestation in the no-till system at a level that does not significantly affect winter wheat yield and does not pose a threat of perennial and invasive weeds when effective herbicide protection is applied