The shortage of construction materials for concrete production on islands far from mainland is a long-standing problem. Coral waste is a by-product during some marine engineering works and it has the potential to be recycled as concrete ingredients. The present work reports the hydration, mechanical and durability-related properties as well as the ecological impacts of marine mortars based on coral waste and metakaolin (MK). Results show that coral waste mortar presents obviously lower compressive strength and chloride resistance than conventional river sand mortar. These defects can be overcome by MK addition due to the formation of carboaluminate, pozzolanic reaction as well as the increased water-retention of paste, which prevents water from being absorbed by coral waste sand (CS) to ensure better uniformity of matrix. Coral waste powder (CP) accelerates cement hydration but reduces the cumulative heat release due to dilution effect. The binary use of CP and MK results in a suspected heat release peak corresponding to the formation of carboaluminate at 26 h. Without sacrifice of the mechanical properties and durability, the coral waste based marine mortar incorporating 10 wt% MK reduces more than 35% non-renewable energy consumption and 40% carbon emission compared to conventional river sand mortar.