The Hout Bay estuary is partly enclosed body of water and has the Disa and Baviaans Rivers flowing into it. The estuary connects the rivers of Hout Bay to the sea.

The estuary forms a changeover zone from river to marine environment and is influenced by the sea (tides, waves and the inflow of salt water) and the rivers (fresh water and sediment). With both sea water and fresh water flowing into the estuary, high levels of nutrients make the river mouth a dynamic and productive natural habitat.

The Hout Bay estuary is vulnerable to pollution coming in from the sea and down the rivers.