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Both climate change and dam operations are affecting water levels in river systems worldwide and their influence can be especially drastic in upper streams, where juvenile salmonids hatch and grow. However, efficient means of mitigating such influence on salmonid populations have not been developed, at least not in a practical manner throughout the world. In this study, we investigated effects of declining water levels and structural complexity on populations of age-0 white-spotted charr (Salvelinus leucomaenis) in tank and pond experiments. Survival of the charr was lower in the shallow tanks (15 cm water depth) than in the deeper ones. Similarly, more fish survived in the tanks with artificial structures (cobbles with Ringlong tape) compared to those without them. The grey heron (Ardea cinerea) was the most frequently observed predator during the tank experiment, and settlement of fish in the shallow ponds increased when artificial structures were provided. These results suggest that declining water levels and the loss of structural complexity may lead to a decrease in populations of white-spotted charr by increasing predation risk and interference competition.