The microalgae sensitivity to exogenous contaminants such as pesticides increases their use as model organisms to appreciate the ecotoxicity of pollutants in aquatic environments and its effect on human health. This study focused on the influence of penconazole pesticide on the chlorophyll a content, cell count, and the biochemical content of Synechocystis aquatilis, Chlorella vulgaris, and Scenedesmus dimorphs. The data indicated that at low pesticide level (0.1, 0.2, 0.4, 0.8mg/  l), the effects declined compared to control, while at higher concentrations (1.6, 2 and 4 mg/ l), the effects were visible. The pesticide had a significant impact on the biochemical contents of the tested algae, particularly at higher concentrations, compared to the control. The three tested species exhibited distinct behaviors in comparison with their controls. Synechocystis aquatilis showed a significant increase in growth between 24 to 28 days, followed by Chlorella vulgaris, and Scenedesmus dimorphus, which exhibited this effect between 32 to 36 days, with samples being taken at four-day intervals. This pattern indicates that Synechocystis aquatilis was the most sensitive microalgae species in response to pesticide pollution in the Qarun Lake habitats.