In contrast to terrestrial habitats and species, which are being comprehensively studied under the HKU Biodiversity Survey and the SUSDEV 21 Habitat Mapping Baseline Survey, marine habitats and species have not yet been subject to a coordinated inventory study. Therefore, marine habitats and species must be characterised by compilation of studies focused on disparate locations, organisms and issues. The following discussion of ecological natural capital stock describes Hong Kong's hard bottom and soft bottom marine environments, and the marine mammals, fishes and invertebrates that inhabit it. Habitats and species of special concern are highlighted.

The character of Hong Kong's hard bottom habitat is strongly dependent on its geographic location, with the most productive areas in eastern and southern waters. Subtidal rocky seabed areas located in the southern and eastern regions of Hong Kong are often encrusted with corals. Subtidal areas with particularly high coral abundance and diversity are those located in the northeastern region of Hong Kong where optimal environmental conditions for settlement, growth and survival for corals prevail (Clarke 1997). The subtidal seabed areas within the Marine Parks at Hoi Ha Wan (Cope and Morton 1988; Zou et al 1992; Morton and Ruxton, 1992) and Yan Chau Tong (AFD 1990) have been characterised as containing well developed fringing coral reefs and rich associated fauna. Shallow hard corals have also been discovered within Penny's Bay (Scott Wilson 2000) and the inner part of the bay appears to support a relatively healthy, simple coral community. In addition to providing habitat for coral settlement, reefs provide shelter, feeding, spawning and nursery areas for a variety of other marine fauna and flora. However, these habitats have been shown to be sensitive to pollution and impacts from development, and if the coral colonies collapse widespread mortality to numerous associated fauna may result.

Subtidal hard bottom habitat located in the western regions of Hong Kong is limited in extent and heavily influenced by the Pearl River. The greatly reduced salinities, increased turbidity, and associated reduced light penetration severely suppresses the growth and survival of hard corals. As a result, only ahermatypic octocorals, ie the soft corals and gorgonians, are commonly found in western waters. Diverse hard bottom habitat in western waters is generally located in areas which are protected from the main effects of the Pearl River discharge (eg southeast Lantau).