The article contains materials derived from the results of the multi-year (2009-2012) studies of algae that spread in different type water bodies of the Nakhchivan AR, in different seasons of year. Due to rising water temperature, development of blue-green and green algae starts in early spring and continues until early fall. Amount of the algae increases, but their vegetation ceases due to the flooding. The intensive development along the river begins after the enlightenment of water. In the water bodies, the least spreading period of blue -green and green algae taxa is in winter period (December-March).