Soil phototrophic microorganisms (algae, cyanobacteria) play a very important role in functioning of anthropogenic systems. They take an active part in soil self-purification by directly absorbing biogenic elements, as well as by stimulating the activity of mineralizing microorganisms at the expense of disengaged oxygen. The research was carried out at a plough field with sod-podzol soil situated near a large pig-breeding farm. Neutralization took place due to natural microbiological processes during the time of disgorging the liquid fraction in the lagoons. Long-term application of manure runoff from pig-breeding farms into plough soil had an impact on species diversity of phototrophic microorganisms, which was considered in the research. Groups of species tolerant to the impact formed in the soil in course of long-term application of liquid manure fraction. The influence of long-term runoff of manure from pig breeding farms on specious diversity of soil phototrophic microorganisms was assessed. In plough soils affected by liquid manure runoff a group of species tolerant to this impact has formed. Their basis is represented by green algae: Klebsormidium flaccidum, K. nitens, Chlorococcum infusionum, Chlorella vulgaris, as well as by the heterocyst-free cyanobacteria Phormidium autumnale and the diatom alga Hantzschia amphioxys. On the surface of plough soil these species make microscopically marked films, i. e. soil “blooming” takes place. General species diversity of microphototrophs in soil of the experimental site is lower than that of the control site. Jaccard coefficient of the experimental and control sites of the field is 47.8%. Nitrogen-fixing cyanobacteria are not represented in the microphototrophic community; it indicates that the natural microcoenosis is damaged in the plough soils and nitrogen content is high.