Abstract Mangroves host many marine species and support fisheries in developing (sub)tropical countries. The suitability of mangrove habitats depends strongly thier the water chemistry. Here, we show how global warming and rising atmospheric CO2 will reduce dissolved oxygen and increase CO2 in mangrove waters. Observations from 23 mangrove‐lined estuaries worldwide revealed that most sites already experience mild (34%–43% of the time) or severe (6%–32%) hypercapnic hypoxia, that is, high CO2 and low oxygen conditions. Hypercapnic hypoxia mostly occurs during low tide, at low‐salinity sites, and in warm tropical regions. Climate change will decrease oxygen concentrations by 5%–35% and increase CO2 concentrations by 8%–60% in mangrove waters by 2100. Overall, hypercapnic hypoxia events will occur more frequently, last longer, and become more severe. These shifts will reduce mangrove biodiversity and deteriorate habitat quality for commercially valuable fish. The strongest impact is expected in tropical developing countries.

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