In 1822, his parents moved to Glasgow where he attended the grammar-school and acquired a good knowledge of the Latin language.
In the summer of 1836 Gardner sailed from Liverpool for Rio de Janeiro, to collect natural history specimens in North Brazil, including plants, minerals, recent and fossil shells, preserved skins of birds, mammals and fishes.
In 1843, the colonial government of Ceylon appointed him as superintendent of the botanic garden in Peradeniya and island botanist.
Here he finished Travels in the Interior of Brazil, principally through the Northern Provinces and the Gold Districts, during the years 1836–41, which was published in London by Reeves Brothers in 1846.
He had also made extensive collections in Ceylon towards a complete Flora Zeylanica, but this was not published because of his early death.