The garden was constructed at the end of the 19th century when the Prüger-Wallner family built a villa at the northern end of Havlíčkova Street, which continues to stand today. The rugged terrain of the garden was landscaped around the villa to form an ornamental garden in a natural-landscape style. The remaining land was used as a utility garden.

After World War II, the garden was left to deteriorate and virtually nothing remained of the original landscaping. After several decades with no conceptual care, the city of Bratislava, in association with partners, started to restore the garden. The garden is regularly landscaped and tidied, and natural furniture, play equipment for children, wooden paths and detailed information boards about the garden's rare biodiversity have been installed. The revitalisation also aims to augment the tree vegetation.

The garden is open to visitors October to March from 8:00 a.m. to 6:00 p.m. and April to September from 8:00 a.m. to 8:00 p.m..

The Prügerka Garden Nature Area is managed by the city of Bratislava/Bratislava Staré Mesto city district.