In order to obtain a higher level of crop yields in crop rotation, there is a need to increase the application of fertilizers and pesticides, which, in turn, creates environmental problems of soil and groundwater pollution by harmful chemical elements and compounds. The purpose of the study was to study the influence of fertilizer systems with different tillage systems on the accumulation of heavy metals and nitrates in the soil and the main products of field crops. Bookmarking and conducting field experiments were carried out in accordance with generally accepted methods of research. The maximum increase in grain yield from the use of N48Р18K18 on the shelf tillage system was – 0.25 (8.7%), grain units – 0.36 (9.9%), feed units – 0.41 (10.3%), digestible protein – 0.02 (5.0%) t/ha of crop rotation area. The use of N48Р18K18 in a differentiated tillage system increased grain yield by 0.34 (12.2%), grain units – 0.49 (13.5%), feed units – 1.12 (28.0%), digestible protein – 0.06 (13.6%) t/ha of crop rotation area. The use of N48Р18K18 in crop rotation with a shallow (mulching) tillage system gave an increase in grain yield by 0.38 (13.6%), grain units – 0.51 (14.2%), feed units – 0.57 (14.5%), digestible protein – 0.07 (15.9%) t/ha of crop rotation area. According to the results of research, the highest increases in mineral fertilizers in terms of productivity were characteristic of a shallow (mulching) background with a characteristic stricter nutrient regime. Our research has not found a significant increase in the content of heavy metals and nitrates in the main and by-products of field crops when applying mineral fertilizers, because their content in the products was within acceptable concentrations. The content of nitrates in the grain of different crops ranged from 18 to 40.4 mg/kg at a maximum concentration limit of 300 mg/kg. High culture of agriculture, improvement and development of new, more effective technologies of application of fertilizers in crop rotation and under each field crop taking into account soil and climatic conditions of the region, biological features of cultures and grades, specialization of crop rotations, etc. prevent environmental pollution. Rational use of mineral and organic fertilizers helps to increase soil fertility and is a major and indispensable factor in significantly increasing plant productivity and crop quality, maintaining an active biological and economic balance of nutrients without contamination of the environment with nitrates and heavy metals.