A shift in the magnitude and timing of animal migrations is one of the most documented ecological effects of climate change. Although migrations are largely driven by spatial variation in resource gradients, few studies connect expected changes in primary production with geographic patterns in migratory behavior. Here, we link lake primary production to the occurrence of sea migrations in the partially anadromous salmonid Arctic char (Salvelinus alpinus L.). We compiled presence/absence records of anadromous char populations spanning productivity and temperature gradients along the Norwegian coast. The probability of anadromy decreased with increasing migration distance, maximum slope of the migration route and lake productivity. There was a significant interaction between lake productivity and migration distance. The negative effect of longer migration distances was more severe in lakes with higher productivity, indicating reduced relative profitability of migration with increased feeding opportunities in freshwater. Lake productivity was mainly driven by terrestrial primary production in the catchment. We predicted future distributions of anadromous char given downscaled temperature and precipitation changes projected by two different emission scenarios and global climate models (GCMs). Projected increases in temperature and precipitation in 2071–2100 increased terrestrial primary production and, compared to the control scenario (1961–1990), decreased the range of anadromous populations. The prevalence of anadromy decreased by 53% in the HadAm3H GCM with the A2 emission scenario, 61% in HadAm3H with the B2 scenario and 22% in ECHAM4 with the B2 scenario. Cross-ecosystem studies (e.g., terrestrial to freshwater) are critical for understanding ecological impacts of climate change. In this case, climate-driven increases in terrestrial primary production are expected to increase primary production in lakes and ultimately reduce the prevalence of anadromy in Arctic char populations.