The diverse landforms, geology, soil and climate in the area have contributed to a diversity of vegetation.  Often the species and the vegetation assemblages are not found anywhere else.  Generally native vegetation in the catchment includes:

• Cumberland Plain Ecological Communities;
• woodland, heaths and open forests on the sandstone of the Hornsby Plateau, Woronora Plateau and along the Harbour foreshores;
• pockets of tall open forest on Wianamatta shales in the higher rainfall areas to the ridgelines north and south of Sydney Harbour;
• mangroves and saltmarsh on tidal flats associated with Parramatta, Lane Cove and Georges Rivers;
• coastal heaths and open forest on sand dunes;
• sub-tropical rainforest (closed forest) of the upper Hacking River and littoral rainforest in isolated pockets along the coastline; and
• sedge-land, and perched and hanging swamps associated with sandstone substrates.

The major direct threats to locally native flora include clearance for urban development and other forms of habitat modification, invasive plants and animals, pollution (including chemical and nutrient pollution of soil and water), an increase in sediment load, altered fire regimes, altered hydrological flows (including sub-soil flow) and climate change.  Salinity impacting on vegetation as a result of non-sustainable urban land uses.  Acid sulfate soils are evident in the catchment and if mis-managed may result in the loss of aquatic and semi-aquatic flora (e.g. seagrasses and mangroves).

Approximately 69,400 ha (i.e. 37 % of the catchment) is covered by native vegetation.  Of the eight major sub-catchments areas the Georges and Hacking River catchments contain the largest areas of remnant vegetation.  A large proportion of the native vegetation in the Georges River catchment is currently either conserved in national parks and Sydney Catchment Authority (SCA) managed land, or occurs on Commonwealth military land.  In contrast, a large proportion of the Hacking River catchment is conserved in the Royal National Park.

Within the SMCMA area there are nine Local Government areas that retain a moderate to large amount of bushland (e.g. 500 - 26,000 ha) relative to other areas in the Sydney Metropolitan catchment.  These LGAs include Bankstown, Baulkham Hills, Camden, Campbelltown, Hornsby, Ku-ring-gai, Pittwater, Sutherland and Warringah.  Of these LGAs Hornsby, Ku-ring-gai, Pittwater, Sutherland and Warringah all incorporate large areas of national park as well as council managed bushland reserves.  Baulkham Hills and Campbelltown have significant amounts (>10,000 ha) of bushland that is not conserved by State or Local Governments.

Local Government areas with a small to moderate amount of bushland remaining (90-260 ha) include Blacktown, Hurstville, Liverpool, Manly, Mosman, Parramatta, Randwick, Ryde and Willoughby.  The largest areas of intact bushland in Manly, Mosman, Randwick and Ryde LGAs are managed by the National Parks and Wildlife Service (NPWS).

Small areas of bushland (less than 90 ha) remain in a number of highly urbanised Local Government areas, including Auburn, Botany Bay, Canterbury, Canada Bay, Fairfield, Holroyd, Hunters Hill, Kogarah, Lane Cove, North Sydney, Strathfield, Waverley and Woollahra.  These areas of bushland are under threat due to their isolation from other areas of bushland, and from urban pressures such as stormwater run-off, weed invasion, impact by feral animals, recreational use and urban infrastructure proposals (e.g. land within designated transport corridors). 

There is minimal natural bushland remaining in or near the inner city.  This includes Ashfield, Burwood, Canada Bay, Leichhardt, Marrickville and Sydney City Council areas..

A significant amount of native vegetation in the Sydney area remains on privately owned land.  Remnant vegetation that is not currently conserved is often under pressure to be removed as infill development and redevelopment occurs.