Littoral benthic primary production is considered the most important energy source of consumers in subarctic lakes. We analyzed essential fatty acid (EFA) and amino acid (EAA) content of 23 littoral benthic macroinvertebrate taxa as well as cladocerans and copepods from pelagic and littoral habitats of 8–9 subarctic lakes to compare their nutritional quality. Pelagic crustacean zooplankton had significantly higher EFA and total FA content (on average 2.6‐fold and 1.6‐fold, respectively) than littoral macroinvertebrates in all our study lakes. Specifically, docosahexaenoic acid (DHA), one of the most important EFA for juvenile fish, was almost exclusively found in pelagic copepods. In littoral macroinvertebrates, only Lymnaea (Gastropoda), Eurycercus (Cladocera), and Gammarus (Amphipoda) contained a low amount of DHA, whereas most littoral invertebrate taxa contained moderate amounts of eicosapentaenoic acid (EPA). The difference in DHA content may explain why so many generalist fish shift their diet to pelagic zooplankton at their peak abundance in mid/late‐summer. Meanwhile, the differences in EAA content between pelagic zooplankton and littoral invertebrates were much lower than for EFA suggesting a wider availability of EAA in subarctic lakes, except for methionine. In the studied subarctic lakes, EFA and EAA variation in consumers was more related to taxon‐specific than lake‐specific characteristics. This indicates that climate‐induced changes in the abundance and community structure of zooplankton vs. littoral macroinvertebrates will be important parameters in determining the availability of EFA and EAA to juvenile fish, and potentially fish production.