Soil algae are often used as bioindicators in assessing the ecological state of the soil. The experiment with alfalfa was carried out on the basis of six-field grain-grass crop rotation in the southern forest-steppe of Western Siberia. The studies were conducted on three agrochemical backgrounds. At the biological background, only organic fertilizer was introduced (straw and cattle manure), at combined backgroundcomplex application of mineral fertilizers in a dose of N20P90, straw and cattle manure, at intensive backgroundfull mineral fertilizer in a dose of N20P90K40 in combination with organic and plant protection products. The object of the study was the algal flora of leached chernozem: from eukaryotes-green (Chlorophyla), yellow-green (Xanlhophyla), diatoms (Bacillariophyla), from prokaryotescyano-bacteria (Cyanobacleriu) or blue-green algae. The analysis of the action of the studied factors was carried out according to the quantitative indicator, the number of cells in one gram of soil (cells/g of soil). When applying the maximum dose of mineral fertilizers, the total number of living algae cells decreased by 70% (102.4 thousand cells/g of soil). When using organic fertilizers (cattle manure, straw) on the same mineral background, the number of cells increased by 98%. The negative impact of agrochemical agents on the algal flora was manifested directly in the year of application; in subsequent years, the number of algae cells increased. Under the alfalfa of the third year of vegetation from the total number of living cells, the share of green and yellow-green accounted for 66-97%. Diatoms were more sensitive to the use of chemicals.