The migratory life history of anadromous salmonids requires successful migration between nursery, feeding and spawning habitats. Smoltification is the major transformation anadromous salmonids undergo before migration to feeding areas and prepares juvenile fish for downstream migration and entry to seawater. We reviewed the effects of climate change on smolt ecology from growth of juveniles in freshwater to early post-smolts in sea. Shift in the suitable thermal conditions by climate change is causing Atlantic salmon to expand their range northwards, while in the southern edge of their distribution populations struggle with high temperatures and occasional droughts. Climatic conditions, particularly warmer temperatures, are affecting growth during freshwater phase in the river. Better growth in the northern latitudes leads to earlier smoltification. Thermal refuges, the areas of cooler water in the river, are especially important for salmonids impacted by climate change. Restoring and maintaining connectivity and suitable diverse mosaic habitat in rivers are important for survival and growth throughout the range. The start of the smolt migration has shifted earlier as a response to increasing water temperatures, which has led to concerns of mismatch with optimal conditions for post-smolts in the sea decreasing their survival. A wide smolt window allowing all migrating phenotypes from early to late migrant’s safe access to sea is important in changing environmental conditions. This is true also for regulated rivers, where flow regulation practices cause selection pressures on migrating salmonid phenotypes. Life history in freshwater affects also marine survival, and there is a need for better collaboration across life stages and habitats among researchers and managers to boost the smolt production in rivers.