Great care was taken to protect wildlife and natural habitats during the planning and building of HKIA, minimising or mitigating environmental impacts wherever possible. Measures included:


- Compensating for trees lost during construction with new trees planted off the airport;
- Supporting the development of a conservation plan for Hong Kong’s Romer's Tree Frog;
- Funding research to help understand population dynamics and abundance of the Chinese White Dolphins in Hong Kong;
- Minimising the impact of marine construction work on marine ecology, particularly with regard to dolphins;
- Supporting a mangrove replanting project in North Lantau to replace mangroves lost during construction; and
- Helping to develop an artificial reef programme and funding the management of the Sha Chau and Lung Kwu Chau Marine Park since 1996.