Human activities threaten aquatic ecosystems and their biodiversity to the extent that we are now living in an era known as the Anthropocene. Fish respond to environmental threats (in part) by changing their physiology, which is reflected across many levels of biological organization. My research focused on the physiology of fishes in vulnerable systems to gain insights into the mechanisms underlying fish responses to human-induced stressors. Specifically, I worked in two threatened systems – coral reef fishes and Pacific salmon – which, although seemingly different, are highly productive and closely tied to the daily lives of humans. These systems are also similarly threatened by warming and fishing activities. In this thesis, I assessed: 1) the nutrient contribution of fish feces to coral reefs, 2) the acclimation capacity and thermal tolerance of a coral reef fish during simulated marine heatwaves, 3) population-specific thermal tolerance of pre-spawning Chinook salmon, and 4) the importance of the heart for aerobic performance in coho salmon. From community-level nutrient inputs down to the cellular function of the heart, my thesis demonstrates that we must consider performance across biological scales when thinking about the conservation and resilience of aquatic ecosystems.