The impact of salmon farming on wild salmon and trout is a hotly debated issue in all countries where salmon farms and wild salmon coexist. Studies have clearly shown that escaped farm salmon breed with wild populations to the detriment of the wild stocks, and that diseases and parasites are passed from farm to wild salmon. An understanding of the importance of these impacts at the population level, however, has been lacking. In this study, we used existing data on salmon populations to compare survival of salmon and trout that swim past salmon farms early in their life cycle with the survival of nearby populations that are not exposed to salmon farms. We have detected a significant decline in survival of populations that are exposed to salmon farms, correlated with an increase in farmed salmon production in five regions. Combining the regional estimates statistically, we find a reduction in survival or abundance of wild populations of more than 50% per generation on average, associated with salmon farming. Many of the salmon populations we investigated are at dramatically reduced abundance, and reducing threats to them is necessary for their survival.