The use of nitrogen fertilizer is becoming a global problem; however continuous fertilization with nitrogen ensures large and constant harvests. An 8 year research (2006–2013) was conducted to evaluate the relationships between differently fertilized cultivated plant rotations. The research was conducted in Lipliunai (Lithuania) in the agroecosystem with nitrogen metabolism in fields with deeper carbonaceous soil, i.e. Endocalcari Endohypogleyic Cambisol (CMg-n-w-can). The research area covered three drained plots where crop rotation of differently fertilized cereals and perennial grasses was applied. Samples of soil, water and plants were investigated in the Chemical Analysis Laboratory of the Aleksandras Stulginskis University certified by the Environment Ministry of the Republic of Lithuania. The greatest productivity was found in a crop rotation with higher fertilization (N32-140). In crop rotation with lower fertilization (N24-90) productivity of cereals and perennial grasses (N0-80) was 11–35 % lower. The highest amount of mineral soil nitrogen was found in cereal crop rotation with higher fertilization. It was influenced by fertilization and crop productivity. The lowest Nmin and Ntotal concentrations in drainage water were found in grasses crop rotation. Crop rotations of differently fertilized cereals increased nitrogen concentration in drainage water. Nmin concentration in water depended on crop productivity, quantity of mineral soil nitrogen, fertilization, and nitrogen balance. The lowest nitrogen leaching was found in the crop rotation of grasses. Cereal crop rotation increased nitrogen leaching by 12–42 %. The usage of all crop rotations resulted in a negative nitrogen balance, which essentially depended on fertilization with nitrogen fertilizer.