The Gardens were begun on their present site in June, 1886. By then, the town of Darwin was 16 years old and the establishment of these gardens was the third formal attempt to select a site which would be suitable to experiment with plants of economic importance. The level area where the gardens are today was once very swampy. The site was chosen after several Chinese gardeners had achieved success with various crops.
The emphasis was on economic gardening and the ornamental plantings which are so much a feature of the Gardens today are a 20th century concept. For the first 30 years, the gardens thrived under the guiding hand of father Maurice and then son Nicholas Holtze. For many years, labour was supplied by prisoners, mainly Aboriginal, with the occassional European and Chinese.
Before World War II, the Gardens were entirely on level ground. During the war, they were used for military purposes and there was an anti-aircraft battery positioned about where the Orientation Centre now stands. By 1944, the gardens were a shambles. Joe Agostini, who worked there before the war, was brought back to begin to repair the damage. All the hillside plantings are post 1946 and Joe added the rockery in the centre of the ring road on the level area.
Severe tropical storms, cyclones in 1897, 1937 and Tracy in 1974 and record wet seasons have wreaked havoc over the years in the Gardens but fortunately those same monsoonal and sub-equatorial climatic conditions are conducive to rapid regeneration and propagation. Even 10 years after the destruction caused by Cyclone Tracy there was limited evidence of that catastrophic event. The raintree supporting the treehouse in the Children's Playground illustrates the tenacity of this particular species (Samanea saman) to survive.
Records dating back to 1884 of the listings of monthly rainfall for the Gardens are archived with the Commonwealth Bureau of Meteorology. The records are incomplete, with data missing in the years between the mid 1890's and the First World War and then from 1922 to 1968. Staff shortages, lack of interest by successive curators, cyclonic activity, aerial bombing during World War II and relocation of the weather stations account for the gaps in the data.
It is not possible to determine the original soil profiles in the Gardens because of the varied utilisation of the land over the years. Soil has been imported from many locations. Portions of the area have been used at various times for a range of activities, including market gardening, experimental crop farming, cattle grazing, as an army camp and as a garbage dump.
Much of the restoration work after Cyclone Tracy was carried out under the guiding hand of George Brown, under the management of the Darwin City Council. The Parks and Wildlife Commission of the NT began management of the Gardens in September 1990. The gardens management is now undertaken by the Department of Natural Resources, Environment and the Arts