Studies of dietary preferences of migratory species are of great importance as these species connect food webs of habitats across the migration route and thus represent trophic relationships between the spatially disjointed communities. Here we described the dietary preferences of threespine stickleback G. aculeatus in the White Sea during the spawning season using stable isotope and stomach content analyses. The two analyses suggested that during the spawning season, when sticklebacks spend the majority of their time inshore, their diet consists mostly of benthic species, while at the beginning of the spawning season when fish migrating from the offshore were feeding on plankton. Additionally, we demonstrated that stickleback eggs contributed greatly to the diet of both male and female fish. Using Bayesian mixing modeling, we showed that dietary preferences in females were broader than in males, and more variable during the spawning season. While guarding their nests, males fed almost exclusively on eggs. Both stomach contents and isotope signatures demonstrate that by the end of the spawning season sticklebacks again increase the consumption of plankton. Isotope analysis proved to be a more reliable tool to trace this change than stomach content analysis. Our results show that stable isotope and stomach content analyses are complementary in understanding seasonal changes in the dietary composition of stickleback.