Fish can alter food web structure through trophic cascades. While most studies conducted in oligotrophic subarctic lakes show strong top–down control on consumers in the presence of fish, several studies undertaken in eutrophic subarctic Lake Mývatn, Iceland, suggest that it is consumer–resource interactions that drive the whole-lake community. Here, we used stable isotopes of carbon and nitrogen from the main food web compartments derived from a 3-month in situ-controlled mesocosm experiment involving two treatments (with and without fish) with three replicates each to determine the effects of fish on the trophic structure of the Lake Mývatn food web. We found that the whole food web trophic structure shifted towards the upper part of the water column (more planktonic habitat) in fishless enclosures. Additionally, the trophic niche of organisms occupying the base of the food web became more diversified when fish were absent, and the trophic redundancy of all taxa decreased (more dissimilar trophic niches). Stronger top–down effects may also result from global warming, producing increased abundance of planktivorous fish in subarctic lakes. Our results indicate that this could lead to a shift in trophic niche and reduced trophic diversity of most food web organisms.