But the method of the cull, in which birds are herded by jetskis and boats toward a line of waiting hunters, has disturbed some members of the public and animal advocacy group SAFE for being cruel and inhuman.
Senior Environment Scientist Stephen Park told a recent council meeting that 15 per cent of the harbour's seagrass beds were being lost every year to black swan grazing.
He highlighted how seagrass meadows played an important role in the productivity of harbour ecosystems, with links to commercially important coastal fisheries.
The long-term impact of swans on seagrass health led to the council agreeing to talk with the Fish and Game Council on population control options. It could involve a maximum population threshold for swans, which have increased from 1900 birds in 1979 to 5100 in 2010.
Dr Dos Santos' study of the site with the highest grazing pressure showed that about 20 per cent of seagrass was removed every year.
Mr Park said comparing seagrass maps taken in 1959 and 1996 showed that 55 per cent of seagrass had been lost in the southern harbour beds, 10 per cent in the northern beds and 70 per cent in the western beds. The loss of seagrass during that period showed a strong relationship with catchment run-off and sediment.