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The global extraction of forest and water resources has led to habitat degradation, biodiversity loss, and declines in ecosystem services. As a consequence, ecological restoration has become a global priority. Restoration efforts to offset this trend, however, are not always effective. One reason is that many restoration projects target single ecosystems and fail to acknowledge functional links between ecosystems. We synthesized current knowledge on links between forest and stream ecosystems, the effect of anthropogenic stressors on these links, and their implications for restoration planning. Many examples show that lateral subsidies, such as invertebrate prey and nutrients, are important in both terrestrial and aquatic environments. Stressors such as commercial forestry, flow regulation, stream channelization, and climate change affect these links and should be considered in restoration planning. Restoration practitioners are encouraged to view adjacent forest and stream ecosystems as one entity.