The site of the Vasse and Wonnerup Floodgates that regulated the flow of water in the estuary from about 1907 inadvertently created the freshwater wetland, were listed on the Western Australian Register of Heritage Places in 2005.
An extensive drainage network has been constructed to protect Busselton and Wonnerup from flooding and to create agricultural land.
The largest breeding colony of black swans in Western Australia (over 150 pairs) is in the estuary.
It is thought that low flows, poor water quality and high phosphorus levels were to blame.
Rainfall washed nutrients downstream to the estuary then a warm spell sparked the growth of algae depleting the water of oxygen, killing the fish.