Long-term population dynamics of three-spined stickleback Gasterosteus aculeatus in the White Sea during the 20th century has patterns similar to that of eelgrass Zostera marina. In this study we address possible mechanisms of such association through analysis of spatial distribution of juvenile stickleback in the wild and their substrate preferences in experimental conditions. Samples from different habitats (Z. marina, Fucus spp.) in 13 localities of Kandalaksha Bay have shown that the juvenile sticklebacks occurred mainly in the eelgrass beds. Their density was significantly lower in fucoids. In the experiments, carried out in August 2008–2009, the juveniles were offered the following types of substrates: brown macroalgae (dense and scarce), eelgrass and control (no substrate). In the experiments sticklebacks also showed a tendency to prefer eelgrass to fucoids, even if the density of the latter was higher. This may explain their higher densities associated with eelgrass in the wild.