The impact of agrotechnical management practices (nutrient and water supply, crop rotation, crop protection, genotype) on the yields of winter wheat and maize and on the soil water and nutrient cycles was studied in long-term experiments set up in 1983 in Eastern Hungary on chernozem soil. The long-term experiments have shown that nitrogen fertilizer rates exceeding the N-optimum of winter wheat resulted in the accumulation of NO3-N in the soil. Winter wheat varieties can be classified into four groups based on their natural nutrient utilization and their fertilizer response. The fertilizer responses of wheat varieties depended on crop year (6.5–8.9 t ha-1 maximum yields in 2011–2015 years) and the genotypes (in 2012 the difference was ~3 t ha-1 among varieties). The optimum N(+PK) doses varied between 30–150 kg ha-1 in different crop years. In maize production fertilization, irrigation and crop rotation have decision role on the yields. The efficiency of fertilization modified by cropyear (in dry 891–1315 kg ha-1, in average 1927–4042 kg ha-1, in rainy cropyear 2051–4473 kg ha-1 yield surpluses of maize, respectively) and crop rotation (in monoculture 1315–4473 kg ha-1, in biculture 924–2727 kg ha-1 and triculture 891–2291 kg ha-1 yield surpluses of maize, respectively). The optimum fertilization could improve the water use efficiency in maize production. Our long-term experiments gave important ecological and agronomic information to guide regional development of sustainable cropping systems.