Objective. To study special aspects of vertical migration of products of biological transformation of organic matter and biogenic elements in sod-podzolic soil under different modes of root nutrition of plants. Methods. Lysimetric experiment, agrochemical, mathematical and statistical. Results. Based on studies conducted in a long-term lysimetric experiment on sod-podzolic soil, periodically washed type of water regime was established, as a result of which 37 mm of moisture, 23 kg/ha of water-soluble humic substances, nitrogen (NO3–) 55 kg/ha, calcium oxide 91 kg/ha and magnesium oxide 26 kg/ha magnesium oxide is lost at the background without inoculation per crop rotation when using mineral fertilization system. The use of microbial preparations reduces the loss of these elements to 33 mm, 20 kg/ha, 52 kg/ha, 83 kg/ha and 25 kg/ha, respectively. It was established that the average infiltration of moisture from the layer 0–155 cm under crops of continuous sowing was 25–37 mm at the background without the use of microbial preparations and 22–33 mm at the background of inoculation. The mineral fertilizer system increased the losses of the soil solution by 9 mm and 7 mm versus the control variants, respective to the backgrounds. The lowest losses of productive moisture were reported in the variants where sidereal fertilizers were used. When replacing the mineral fertilization system with sidereal-mineral and organo-mineral fertilizers without compromising the yield of crop rotations, it is possible to reduce the loss of productive moisture by 1.5 times, reduce the loss of labile soil organic matter by 1.7–1.8 times, nitrate nitrogen by 8–10 %, calcium by 18–24 % and magnesium by 40–50 %. Due to the use of biopreparations, there is a reduction in losses of nitrate nitrogen by 5–18 %, magnesium — by 5–14 %, calcium — by 6–16 %. Conclusion. To reduce non-productive losses of moisture, water-soluble organic matter and biogenic element compounds, it is advisable to use green mass of green manures and microbial preparations at the background of the mineral system and fertilizer system NPK+manure. The use of microbial preparations helps to reduce the loss of nitrate nitrogen by 5–18 %, magnesium — by 5–14 %, calcium — by 6–16 %.