Sea level rise, marine acidification, nutrient runoff, degraded benthic sediment and water quality, and increment in emerging pollutants like microplastics, pharmaceuticals and personal care products (PPCP) along the coastal beaches of Southeast Asian countries (SeAC) Thailand, Cambodia, and Vietnam are resulting into imminent diminish or extinction of coral reefs. Due to lack of scientific regional collaboration and evidence-based research, fate and distribution of coral reefs and marine ecosystem services have not been effectively managed in these SeAC. Hence, the main objective of this research is to manage risk and enhance resilience of the coral reef. A trans-disciplinary team through appropriate mix of engineering, socioeconomic significance, and policy framework will research on identifying the gaps, opportunities and threat in coral reef management. Scientific evidence-based research will be undertaken to understand the impact of benthic sediment and water quality, emerging pollutants, and human induced pressure on coral reef. A successful completion of this research is expected to i) understand the present and future scenario of the coral reef abundance and diversity, and ii) assist in capacity development and policy formulation with evidence-based scientific outputs in managing coral reef and marine ecosystem services. Outcomes are expected to be beneficial in establishment of collaborative research platform, one of the first, in coral reef management in SeAC.