The initial destruction of the Cooks River came about as a result of forest clearance for farming, starting in the late 1700s. The Turpentine-Ironbark Forest and the Floodplain Forest grew on the best agricultural soils and were sought first. Reverend Richard Johnson, chaplain of the colony, acquired land at Canterbury, which was cleared for cultivation in the 1790s (Benson et al 1999:22).

The timber of the Swamp Oak trees growing in the Floodplain Forests was used to make roof shingles. Also desirable were the bigger Eucalyptus trees in the Turpentine-Ironbark Forest. Clearing for agriculture continued throughout the nineteenth century.

In the early 1800s, mangrove wood was burnt to supply barilla, an alkaline ash used for the manufacture of soap. In 1828 there were ‘two or three manufactories of soap’ at Botany Bay, though by 1831 it was reported that ‘The soap boilers still suffer considerable restriction from the insufficient supply of mangrove ashes’ (Benson & Howell 1990). The extensive mangrove forests in the estuary of the Cooks Rivers must have been an important source of wood for these factories (Benson et al 1999:23).