Cyanobacteria are characterized by a very high tolerance to environmental factors. They are found in salt water, fresh water, thermal springs, and Antarctic waters. The wide spectrum of habitats suitable for those microorganisms is related to their particularly effective metabolism; resistance to extreme environmental conditions; and the need for only limited environmental resources such as water, carbon dioxide, simple inorganic salts, and light. These metabolic characteristics have led to cyanobacterial blooms and the production of cyanotoxins, justifying research into effective ways to counteract the excessive proliferation of these microorganisms. A new and interesting idea for the immediate reduction of cyanobacterial abundance is to use natural substances with broad-spectrum biological activity to restore phytoplankton diversity. This study describes the effects of selected monoterpenoid derivatives on the development of cyanobacterial cultures. In the course of the study, some compounds ((+/-)-citronellal, (+)-alpha-pinene) showed the ability to inhibit the colonization of the tested photosynthetic bacteria, while others (eugenol, eucalyptol) stimulated the growth of these microorganisms. By analyzing the results of these experiments, information was obtained on the mutual relations of cyanobacteria and the tested monoterpenes, which are present in the aquatic environment.