The Botany Bay catchment extends from Prospect Reservoir near Blacktown and extends to the south-west and south of Sydney. The catchments for the Cooks River, Georges River and Woronora Rivers are also part of the Botany Bay catchment.

The low ridge between Port Hacking and Botany Bay forms the south-eastern boundary of the catchment

There are some 25 local government areas within the Botany Bay catchment, including Fairfield, Liverpool, Campbelltown, Bankstown, Canterbury, Marrickville and Sutherland Shire.

The Botany Bay catchment extends across some 1165 square kilometres. It is bounded by the Parramatta River and Sydney Harbour catchments in the north, the Hawkesbury-Nepean catchment in the west and the Hacking River catchment in the south.

Botany Bay and its catchment waterways are subject to ongoing threats due to nutrient and sediment-laden run-off from various non-agricultural land uses. A substantial part of the catchment is highly developed with almost 40% of its area being used for urban, industrial or commercial purposes.  Pollutants of concern are nitrogen, phosphorus and total suspended solids.

Botany Bay and its catchment are significant, being home to many endangered species and communities. Of significance is the  Ramsar-listed wetlands within Towra Point Nature Reserve which are home to many species of migratory birds.

Botany Bay is important for recreational, water based activities and cultural heritage.