The School offers a variety of Master's Degree programs.

Mathematics and computer science: applied mathematics, numerical techniques, economic mathematical and information support, computer mathematical support, mathematical simulation information systems and technologies, programming engineering, computer methods of analysis and synthesis of project solutions, and business information systems

Physics: theoretical physics, medical physics, earth and planetary physics, physics methodology, nanostructure physics, and nanoscale system physics

Chemistry: bioorganic chemistry, organic chemistry, physical chemistry, analytic chemistry, environmental chemistry, chemical expertise and ecological safety, organoelemental compound chemistry, energy and resource conservation processes in chemical technology, and petroleum chemistry

Biology: hydrobiology and ichthyology, developmental biology, cell biology, marine biodiversity, and environment conservation

Geography: nature management and protection

Informatics and computers: design, analysis and synthesis methods

Soil science: land classification and soil conservation

The School also has also Master's degree programs in geology, ecology and nature management, biotechnology, and applied hydrometeorology.

Since 2012, a new Masters Degree Program in English is offered in Marine Biodiversity and Aquatic Environment Conservation. It is an interdisciplinary program taught by the faculty from several departments: Biodiversity and Marine Bioresources, Ecology, Cell Biology and Genetics, and Soil Science in association with professors from the Russian Academy of Sciences. The courses offered by the program cover various aspects of marine and fresh water biology: diversity of invertebrate animals and plants, processes and structure of marine ecosystems, soil formation in the sea and on shore, and impacts of the environment on cells, tissues and physiology of organisms. This program prepares professionals in biology and ecology to work in research and R&D institutions, innovative businesses specializing in this field and higher education institutions.