The lake lies mostly within the boundaries of Boonderoo and Kanandah Stations which were established in the 1960s and have been running cattle since 1973.

The lake has filled in 1975 following heavy rain events further north near Leonora after a cyclone.

The rains filled both Lake Braeside and Lake Rebecca to overflow down Ponton Creek to fill Boonderoo and expand out to an area of between 50 square kilometres (19 sq mi) to 80 square kilometres (31 sq mi).

[2] Lake Boonderoo is an important wetland for birds and invertebrates as it dries out and becomes increasingly saline.

In 2005 the lake was found to have a 250 hectares (618 acres) infestation of the invasive weed, the tamarisk tree.