The article discusses a comparative study on the characteristics and content of lipids and fatty acids (FAs) in White Sea Herring fisheries from Onega and Kandalaksha bays of the White sea, Russia which differs from its trophoecological conditions. The comparative research explores the Kandalaksha and Onega bay's inlets, phytoplankton and bacterioplankton activity. The study concludes that herring fisheries from Kandalaksha bay have higher content of total lipids (TLs) than of the Onega Bay.