Winter represents a challenging season for animals in boreal streams and is a period with low temperatures, extremely low levels of primary production, low metabolic rates of ectotherms, and little light. Yet, stabile ice cover provides shelter for salmonids residing in rivers. Despite low light levels in winter, stream salmonids are mainly nocturnal, which protects them from diurnally active predators. Climate change adds unpredictability, increases frequency of winter floods, and can reduce the time that salmonid embryos need to develop until hatching and emergence. These changes can increase natural winter mortality and cause recruitment failures in populations that already are under severe pressure from environmental changes and fishing. We identify a need to better monitor egg and fry survival to predict the effects of changing temperature and environmental stressors such as loading of organic material or flow regulation. Availability of microhabitats for sheltering during winter is crucial and should be considered in restoration efforts focused on recovering threatened salmonid populations. The importance of habitat quality will increase in an unpredictable environment, and both management attention and research on the early life-history phases of salmonids are needed to understand how climate change-induced environmental changes affect fish through winter processes.