The site was originally farmland. Council resumed the site in the late 1950s. Part of the site was used to create the Lake Macdonald water supply.
The site was used to dump rubbish until local resident Ida Duncan approached council for permission to clear the site. With the help of other locals, Ida Duncan cleared the area of weeds and car bodies.
Funding from a government community employment program was used to start construction of the botanic gardens in 1987.
When the program ended, council appointed two full time staff to continue construction and maintenance of the gardens. Former Noosa Shire Parks Curator, Bob Bickley designed the layout of the gardens. Council has funded the gardens since 1988.
The Noosa Botanic Gardens officially opened to the public in August 1990.