Equally effective way to achieve sustainable farming and the challenge set by the European Commission on 20 May 2020: proper crop rotation and thus reduction of the quantity of on-farm chemicals. Long-term stationary field experiments were established in 1966 at Vytautas Magnus University Experimental Station (54°53′ N, 23°50′ E). The study was conducted with intensive, three-course, field rotation with row crops, for green manure crop rotations, and rye monoculture as well during the last 5-year period of a 50-year investigation to determine the effect of crop rotation combinations and rye monoculture on weed density and seed bank and grain yield. In cereal crops, weed counting was performed twice: weed density was determined before the application of herbicides, and weed counting was done before the harvest. Weed seedlings were counted, their botanical species were determined, annual and perennial weed number was estimated. Weed seed bank was established before primary tillage in soil. The results obtained confirmed the hypothesis that with climate change and intensive farming, long-term crop rotations are likely to increase crop productivity, reduce weeds and weed seed banks in the soil, and thus contribute to maintaining agroecosystem sustainability. The winter rye 1000 grain weight and yield decreases as weed mass increases showing strong negative correlations: y = 475.56 − 11.93x, r = −0.91, p ≤ 0.05; y = 82.97 −14.82x, r = −0.97, p ≤ 0.01. Reseeding of rye crops leads to a growing prevalence of weeds such as Equisetum arvense L. and Mentha arvensis. Crop structures these days are dominated by cereals, which inevitably increase the spread of weeds, and therefore, the importance of crop rotations increases in the context of intensive farming.