Climate change is rapidly altering fisheries supporting aquatic ecosystems. The implications for food security depend not only on harvest biomass but also concentrations of nutrients and toxins in fish. Using brook trout from Adirondack lakes (New York, USA), we tested whether ongoing lake deoxygenation trends will affect fish muscle omega-3 fatty acids, selenium, and mercury concentrations. Across space (16 lakes: 1 year) and time (6 years: 1 lake), anoxia decreased selenium and was associated with elevated fish mercury, with no effect on omega-3 content. Because selenium may mitigate some end points of mercury toxicity, highly variable Se:Hg molar ratios (0.70-35.79) in neighboring lakes may have health risk implications. For fish consumers, ongoing lake deoxygenation under climate change could potentially reduce selenium intake while enhancing mercury exposure. Simultaneous alteration of beneficial compounds and toxins by environmental change complicates the development of fish consumption advisories to safeguard public health in a warming world.