Aquatic ecosystems have been extensively modified by human activity. The resulting degradation of aquatic habitats has led to devastating declines in fish biodiversity, with freshwater-dependent species suffering disproportionately. Restoration has become an increasingly popular strategy aimed at remedying the degradation of aquatic systems and reversing declines in fish biodiversity. Billions of dollars are spent on aquatic restoration each year within the United States alone, and yet the majority of restoration projects do not achieve success in reaching the goals of mitigating degradation and halting fish biodiversity loss. Restoration monitoring efforts typically rely on population- and community-level metrics that cannot respond to restoration on the short temporal scales that projects are usually monitored (< 2 years), making it difficult to evaluate success or garner lessons that can be applied to future projects. Physiology is able to “fill in the gaps” that traditional monitoring cannot as it is mechanistic and can respond to environmental changes across multiple scales, particularly within short timeframes. Physiology can be thought of as a “filter,” whereby any change within the environment must first affect individual fish at the physiological level before it can affect fish at the population or community level. We discuss this link between physiological responses and population-level effects and ways in that physiology might be integrated into the restoration process. We propose that the integration of physiology into restoration monitoring is essential to improve the success of restoration projects for fish.