Southeast Asian coral reefs in Thailand, Cambodia, and Vietnam are critical socio-economic assets, generating over USD 11 billion annually. However, they face escalating threats from climate change and local anthropogenic stressors. Synthesising empirical field data, remote sensing and research outcomes from the APN CRRP2019-08MY-Khanal project, this review reveals significant regional degradation. Specifically, Vietnam has lost 11–12% of its coral cover since the early 2000s, with 48% now classified as vulnerable, while 37% of Thailand’s reef areas were reported damaged in 2021. Severe localised stressors drive this decline, including high land-based pollution—such as an average sediment yield of 77.67 tons/ha/year in Vietnam’s Cai River basin—and emerging chemical contaminants, such as UV filters, that alter the photodegradation of coexisting pollutants. Additionally, mass over-tourism has caused localised ecosystem collapse, necessitating drastic emergency interventions, such as the closure of Maya Bay in Thailand. Although ambitious national targets exist, such as Vietnam’s goal to expand Marine Protected Areas to 6% by 2030, implementation is severely hindered by weak enforcement, funding shortfalls and critical gaps in restoration guidelines. To secure these ecosystems, this review advocates transitioning to resilience-based management, establishing sustainable financingand strengthening the science-policy interface to translate empirical risk assessments into adaptive, localised governance.