The role of nanotechnology in solving environmental problems is increasing, and there is a need for additional research in this area. One of these environmental problems is soil salinization. During salinity stress, germination, growth and development ofplants slow down, and the quantity of pigments, chlorophyll and carotenoids in leaves decreases. So does the activity of such important physiological processes as photosynthesis, respiratory processes and enzyme activity. There are several ways to improve the salt tolerance of cotton. The cotton varieties can be improved genetically, or another way is to increase the stability of seeds or seedlings by chemical, biological or physological methods. At the early stages of development cotton seedling are very sensitive to salinity and other stress factors. The study investigated the effect of Al nanoparticles on the pigment composition in cotton seedling leaves and on the enzyme activity (ascorbate oxidase, polyphenol peroxidase and guaiacol-dependent peroxidase) in soil samples, collected in different areas of the Mugan plain. It was found that cotton seeds develop well in saline soils if treated with Al nanoparticles. Significant changes were observed in the plant development and in the kinetics of physiological processes. The quantity of chlorophyll pigments a and b in cotton sprouts (mainly at three leaf stages) increased, and the change in enzyme activity occured. Thus, during salinity stress the influence of basic enzymes, such as ascorbic peroxidase, increased in sprouts but decreased in leaves if the cotton plants are cultivated in saline soils with Al nanoparticles. The decrease in the activity of polyphenol oxidase and guaiacol-dependent peroxidase was insignificant.