Phytoremediation is one of the effective technologies for removing pollutants from the aquatic environment. Toxic compounds such as chlorpyrifos can affect the physiological processes of aquatic plants, causing secondary oxidative stress in plant tissues. Macrophytes, like other organisms inhabiting the contaminated ecosystem, have developed a system of defense mechanisms, thanks to which plants can still exist in their natural ecosystem. Our research is a summary of the previously presented results of the effectiveness of purifying contaminated water with chlorpyrifos in the phytoremediation process and the second type of phytoremediation supported by microorganisms, which intensify the process of removing contaminants from the environment. This research concerned changes in nonenzymatic and enzymatic antioxidants in Canadian seaweed, needle spikerush and water mint caused by chlorpyrifos. The research determines changes in the total concentration of polyphenols, flavonoids and dyes (chlorophyll A, chlorophyll B, anthocyanins and carotenoids) as well as differences in the activity of guaiacol peroxidase and glutathione S-transferase. The analysis of the results showed an increase in the content of polyphenols and flavonoids. The reverse trend was observed in the case of the pigment content. The appearance of chlorpyrifos in the environment caused an increase in the activity of the examined enzymes. The process involving microorganisms that were obtained from places contaminated with pesticide proved to be more effective. This shows the cooperation of species living in an investigated ecosystem.