The results of the comparative analysis of chloroplast ultrastructure and analysis of photosynthetic pigments content in floating and submerged leaves of water fern Salvinia natans (L.) All. at the different stages of ontogeny are presented. The ultrastructure of photosynthetic organelles and pigments content are significantly different in floating and submerged leaves. The chloroplasts of parenchymal cells of floating leaves have a well-developed membranous system with many grana and contain many starch grains. Submerged leaves were shown to form smaller chloroplasts with low starch content in the stroma. A smaller number and smaller size of grana complexes in chloroplasts were marked, too. Destructive changes in the photosynthetic membranes of chloroplasts in both types of leaves were observed at the stage of sporocarps formation. The content of photosynthetic pigments in the floating leaves was twice higher than in the submerged leaves, and at the certain stages of ontogeny three times higher. During development of the plant, a content of photosynthetic pigments raised up in the floating leaves. At the stage of sporocarps formation, some reduction of chlorophylls and carotenoids content in submerged leaves occurred. In this article, we discuss the relationship between the identified differences and the functional activity of floating and submerged leaves during growth and development of water fern S. natans.