The study is concerned with the lipid and fatty acids profile in juveniles of the threespine stickleback (Gasterosteus aculeatus) from two spawning grounds in Keret Archipelago of Kalandalaksha Bay of the White Sea: a highly productive inlet with the dense eelgrass population (Seldyanaya Inlet) and a shallow lagoon with eelgrass population of average density (Sukhaya Salma). The differences in juveniles from these habitats in the content of reserve triacylglycerols, membrane phospholipids, polyenic, physiologically important, 22:6ω-3 and 20:5ω-3 fatty acids, and indexes of essential 18:3ω-3/18:2ω-6 and ω-3/ω-6 polyenic fatty acids were revealed. The obtained results can be explained by the differences in food composition (on the level of species composition and abundance of forage organisms and their lipid and lipotrophic composition) or by the effect from abiotoc factors (mainly temperature), which influence the intensity of metabolic processes in juvenile stickleback.