The ecological functionality of the East Asian-Australasian Flyway is threatened by the loss of wetlands which provide staging and wintering sites for migrating waterbirds. The disappearance of wetland ecosystems due to coastal development prevents birds from completing their migrations, resulting in population declines, and even an eventual collapse of the migration phenomenon. Coastal wetlands are also under threat from global climate change and its consequences, notably sea level rise (SLR), extreme storm events, and accompanying wave and tidal surges. The impacts of SLR are compounded by coastal subsidence and decreasing sedimentation, which can result from coastal development. Thus, important wetlands along the flyway should be assessed for the impacts of climate change and coastal subsidence to plan and implement proactive climate adaptation strategies that include habitat migration and possibility of coastal squeeze. We modelled the impacts of climate change and decreasing sedimentation rates on important bird habitats in the Mai Po Inner Deep Bay Ramsar site to support a climate adaptation strategy that will continue to host migratory birds. Located in the Inner Deep Bay of the Pearl River estuary, Mai Po's tidal flats, coastal mangroves, marshes, and fishponds provide habitat for over 80,000 wintering and passage waterbirds. We applied the Sea Level Affecting Marshes Model (SLAMM) to simulate habitat conversion under two SLR scenarios (1.5m and 2.0m) for 2050, 2075, and 2100 for four accretion rates (2mm/yr, 4 mm/yr, 8 mm/yr, 15 mm/yr). The results showed no discernible impact to habitats until after 2075, but projections for 2100 show that the mangroves, marshes and tidal flats could be impacted in almost all scenarios of SLR and accretion. Under a 1.5m SLR scenario, even at low tide, if accretion levels decrease to 4 mm/yr, the tidal flats will be inundated and with a 2 mm/yr accretion the mangroves will also be inundated. Thus, important shorebird habitats will be lost. During high tide the ponds inside the nature reserve, which are intensively managed to provide high tide roosting sites and other habitats for waterbirds, will also be inundated. Thus, with a 1.5m SLR and declining sedimentation the migratory shorebirds will lose habitat, including the high tide roosting habitats inside the nature reserve. The model also indicates that the fishponds further inland in the Ramsar site will be less impacted. Most fishponds are privately owned and could be developed in the future, including into high rise apartments; thus, securing them for conservation should be an important climate change adaptation strategy for Mai Po, since they provide essential habitats for birds under future climate change scenarios. But Mai Po is only one steppingstone along the EAAF, and hundreds of other wetlands are also threatened by encroaching infrastructure and climate change. Thus, similar analyses for the other wetlands are recommended to develop a flyway-wide climate-adaptation conservation strategy before available options become lost to wetland conversion.