Balance of nitrogen and magnesium was monitored in a small - plot experiment which was established in year 2008-2009 on experimental research base of SPU Nitra - Doln Malanta. Experiment was under integrated (IS) and ecological (ES) farming system. In both farming systems were two variants: fertilized and non fertilized. Crop rotation was within six-field. We used subsequent crops in the experiment: winter wheat, spring barley, lucerne, pea, silage corn and faba bean. Fertilization was performed on the basis of soil and plant analyses using balance method. In both farming systems was applied farm yard manure (40 t. ha(-1)). In integrated system were applied except organic manorial also industrial fertilizers: LAV 27, superphosphate and potassium salt. Inputs of nutrient included nutrients from seed, organic and industrial fertilizers, by nitrogen symbiotic fixation, asymbiotic fixation and precipitation. Outputs of nutrients were represented by off-take by crop yield, off-take by by-product. Other outputs of nitrogen were also calculated with leaching, volatilization and denitrification. Then balance was calculated as difference of total inputs and outputs. Percentage nutrient substitution was calculated as total intputs divided total outputs and multiple handrid. In integrated farming system the percentage of nitrogen substitution on non fertilized variant and on fertilized variant was 60.31% and 98.22% respectively. Percentage of nitrogen substitution on ecological farming system reached on the level of 68.05% on non fertilized variant and 84.40% on fertilized variant. Percentage of magnesium substitution amounted on I/0, I/OR, E/0, E/OR was 2.54%; 34.54%; 1.98%; 30.94% respectively.