Leptospira interrogans spirochetes belong to a group of pathogens of particularly dangerous infections that cause leptospirosis in many species of wild, farm and domestic animals, as well as humans. Significant economic damage caused by this disease to livestock around the world, numerous cases of death from leptospirosis, and mainly waterborne transmission of the infection determine the topicality of studying all the aspects of the existence of L. interrogans in freshwater ecosystems. The objective of our study was to determine the nature of ecological relationships between L. interrogans and green algae. We used green algae of the Desmodesmus brasiliensis species as a model object. In the experiments, sterile algae culture filtrates were added to L. interrogans containers grown at 27–28 °C. Comparison of the content of spirochete cells in the experiment and control samples, conducted 24 hours after exposure, showed that the reproduction of L. interrogans is markedly inhibited in the samples containing algae secretions at the dilutions of 1:10 and 1:100. In order to reduce resistance to the allelopathic influence of D. brasiliensis algae, leptospira strains were located as follows: Pomona, Australis, Hebdomadis, Canicola, Sejroe, Icterohaemorrhagiae, Grippotyphosa, Tarassovi. The obtained results indicate a complex intraspecific structure of L. interrogans and their high ecological plasticity. In addition, experimental data indicate that, due to the release of biologically active substances into the aquatic environment, green algae have the potential to affect the dynamics of a number of leptospirosis pathogens in situ. Given the important epidemiological and epizootic significance of pathogenic leptospira, further research is necessary to determine the patterns of their interactions and existence in the environment.