The indigenous vegetation communities originally associated with Manly lagoon and its tributaries have been heavily altered by urban development. There has been widespread introduction of ornamental exotic species such as Coral Trees which seasonally contribute very substantial amounts of leaf matter into the tributaries and the lagoon to the detriment of water quality. Weed infestations are common throughout the area, particularly where maintenance is less intensive, detracting from the water quality, habitat value and recreational amenity of the waterways.
A recent Survey of the vegetation around Manly Lagoon found that:
Indigenous Species 67
Noxious Weeds 26
Exotic species l40
Total number of species 222
Endangered plant species: Tetratecha grandulosa (community of endangered Duffy's forest vegetation) found at the top of the catchment