Studies of dietary preferences of migratory species are of great importance as these species connect trophic webs of habitats across the route of migration and thus represent trophic relationships between the spatially disjointed communities. Here we describe dietary preferences of the White Sea threespine stickleback Gasterosteus aculeatus during the spawning season using stable isotope and stomach content analyses. Both analyses indicated that during the spawning season, when sticklebacks spend most of the time in the nearshore, their diet significantly consist of benthic species in contrast to the start of the spawning season when fishes migrating from the offshore are feeding on zooplankton. Also, we show that stickleback eggs contribute greatly to the diet of both male and female fishes. Using Bayes mixing modelling we show that dietary preferences in females were broader than in males, and more variable during the spawning season. Males fed on eggs almost completely while guarding their nests. Both stomach contents and isotope signatures demonstrate that by the end of the spawning season sticklebacks again increase consumption of plankton, and isotope analysis proved to be more reliable tool to trace this change than stomach content analysis. Our results show that stable isotope and stomach content analyses well supplement each other in understanding of seasonal changes in dietary composition of stickleback.