Globally, coastal forested wetlands are increasingly affected by relative sea level rise. However, the mechanisms underlying coastal wetland degradation remain unclear. Using the eddy covariance approach, we evaluated the long-term (i.e. 2009–2019) net ecosystem exchange (NEE), associated hydrology, and ecosystem structural changes in a forested wetland in North Carolina, USA. We quantified tree mortality in response to changes in hydrology. The ecosystem shifted from a net C sink (NEE = − 3.68 Mg C ha−1 yr−1) pre-2010 to a net C source (NEE = 0.87 Mg C ha−1yr−1–7.59 Mg C ha−1 yr−1) afterward. We ascribe the ecosystem C loss to increasing tree mortality (i.e. from 1.6% in 2009 to 45.8% in 2019), partly due to relative sea level rise (R2 = 0.62). Tree mortality, and consequent shift of NEE, provide early warning signs of a transition in this ecosystem more than 20 km inland from the coast.

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