This study provides a rather new approach to research on a portion of general biological production of marine ecosystems, namely on primary production. The methodology presented consists of two blocks of techniques. The hydrological block provides for an estimate of the amounts of basic water masses, the estimate being based on the salinity and δ18O stable isotope value. The techniques of the ecosystem block provide for a calculation of primary production based on the water mass composition, nutrients concentrations in the cores of the water masses, and changes in nutrients reserves. The rate of the nutrients reserve change is corrected by the non-productive component caused by the inflow or outflow of the nutrient as a result of advection or exchange with underlying layers. Another correction is related to nutrient regeneration going in parallel to photosynthesis. The technique was tested and verified in the waters around the Svalbard archipelago. By using a combination of δ18О isotope parameter (with an intention to add δ2H in the future), salinity, and nutrients composition, the present methodology allows to consider the domain of the marine ecosystem comprising its hydrological, hydrochemical, and hydrobiological (phytoplankton) processes as a single system of their relationships.