A research fellow at the Plant Functional Biology and Climate Change Cluster of the University of Technology, Sydney, Dr Paul Gribben, says it's essential we don't overlook the importance of the harbour to marine life in our rush to use the waterway.

A specialist in marine community ecology, Gribben says 90 per cent of the biodiversity in the harbour - the range of plants and animals it contains - is there because of habitat-forming species. These species form structures and environments that provide food and shelter.

While there are several types of habitat-forming species, there are two main categories in Sydney Harbour: macrophytes and invertebrates.

Macrophytes are aquatic plants such as seaweed or seagrass and are central to the functioning of healthy ecosystems. They play an important part in the nutrient cycle, consuming carbon dioxide and producing oxygen to help with the decomposition of organic matter. They provide food for big and small species, attracting smaller plants and animals for larger species to eat, while offering refuge for others from predators. They are also very important nursery grounds for juvenile fish, many of which are important for recreational fishing.

The other type of habitat-forming species are invertebrates, including small molluscs and crustaceans that colonise rock formations. In these environments, hundreds of individual organisms colonise a rocky area to create a complex matrix, which houses a variety of species.

These ecosystems promote biodiversity and the filter-feeding molluscs also remove and break down many of the toxins polluting the water, meaning they are essential to the health of the harbour.

Conserving macrophytes begins with finding and monitoring them.

''It is important to know where these colonies are and how much they've changed so we can manage them over time,'' Gribben says. ''Once we have a detailed map, we can potentially remediate those habitats that have been lost.''

Conserving seagrass areas requires a holistic approach to cleaning up the harbour. Pollution needs to be decreased, sediment levels lowered and ecosystems protected from recreational and commercial overuse, Gribben says. He says conserving seagrass areas is the best way to conserve the harbour's health.

Some of the threats to invertebrate habitats are the same as those facing the macrophytes, such as overpollution, but people also harvest molluscs to collect and eat. Ensuring that human impact doesn't destroy these ecosystems is key.

Developing strategies for communities to help protect and promote these ecosystems into the future is a high priority, Gribben says.

''From a conservationist's perspective, these habitats are the most important parts of maintaining our harbour's health.''