Our current work on hypoxia and acidification encompasses a number of processes, temporal patterns, and scales. We have developed a computer-controlled laboratory system that allows us to mimic the natural fluctuations in dissolved oxygen and pH that organisms experience in shallow water. This ‘diel-cycling hypoxia and acidification’ is a result of day-night variation in the net balance between oxygen production through photosynthesis during daylight and respiration by organisms throughout the day and night. By combining experiments using this system with field collections and experiments in Chesapeake Bay, we have found that even a few hours of hypoxia each day can increase the prevalence and intensity of Dermo, a disease caused by the protistan parasite, Perkinsus marinus, that has reduced oyster populations in Chesapeake Bay and increased the difficulty of restoration efforts. We have also found that low oxygen reduces filtration and growth rates of oysters, but the effects of acidification are more complex. Elevated carbon dioxide can slightly stimulate filtration rates and effects on growth depend on factors such as oyster age and duration of exposure. Our experiments with Atlantic and inland silverside fishes also seek to understand the combined effects of hypoxia and acidification, including the potential for acidification to affect the sensitivity of fish to low oxygen and the ability of fish to acclimate to these stressors. We are also studying the patterns and potential effects of diel-cycling hypoxia and acidification in ponds that form in tropical mangrove islands in Belize and Panama. At larger scales, we are using data on estuaries and coastal and inland seas to better understand global patterns and effects of nutrient enrichment and hypoxia on fish abundance and fisheries catches.