We compare carbon budgets between a herbivore-dominated and a microbial loop-dominated food web and examine the implications of food web structure for fish production. We use the southern Barents Sea as a case study and inverse modelling as an analysis method. In spring, when the system was dominated by the herbivorous web, the diet of protozoa consisted of similar amounts of bacteria and phytoplankton. Copepods showed no clear preference for protozoa. Cod, a predatory fish preying on copepods and on copepod-feeding capelin in spring, moderately depended on the microbial loop in spring, as only 20 to 60% of its food passed through the microbial loop. In summer, when the food web was dominated by the microbial loop, protozoa ingested 4 times more bacteria than phytoplankton and protozoa formed 80 to 90% of the copepod diet. Because of this strong link between the microbial loop and copepods, the young cod’s main prey item, young cod depended more on the microbial loop than on any other food web compartment, as > 60% of its food passed through the microbial loop in summer. Adult cod relied far less on the microbial loop than young cod as it preyed on strictly herbivorous krill in summer. Food web efficiency for fish production was comparable between seasons (≈ 5×10-4) and two times higher in summer (5×10-2) than in spring for copepod production.