A comparative study of the lipid metabolism in Atlantic salmon fingerlings staying after hatching near their spawning redds along the banks of the Varzuga River main channel (at rapids and riffles) and those who had migrated to tributaries – the Arenga, the Pjatka and the Falaley. The choice of habitats by fingerlings after hatching and dispersal affects the quantitative characteristics of lipids and fatty acids, and is supported by the organism’s adaptive systems, including variations in the ratios of individual lipid and fatty acid classes within physiological limits. Fingerlings from the Pjatka had higher length-weight values, the energy/structural lipids ratio(TAG+ECHOL/PL+CHOL), and the ratio of essential fatty acids 18:3ω-3/18:2ω-6 as compared to fish from other studied biotopes. The combination of ecological and trophic conditions (temperature, water flow rate, depth, riverbed particle size composition and fouling, species composition and amount of food items, and their availability) in the Pjatka are more favorable for the growth and development of fingerlings. The identified biochemical differences between the fingerlings that had migrated to the tributaries and those remaining along the main channel banks may be the basis for the formation of steady fish differentiation into groups with different lipid status and length-weight indices during further development (in fish aged 1+ and 2+). This differentiation in 0+ Atlantic salmon can be considered as a start of intrapopulation heterogeneity, affecting further choices on the fish life strategy.