The Museum Gardens were developed in the grounds of St Mary's Abbey and opened in 1830 as part of the new Museum development by the Yorkshire Philosophical Society.

The gardens were designed in the "Gardenesque" style by landscape architect, Sir John Murray Naysmith.  The layout was designed to show off the buildings of the Museum and Abbey while providing spaces for displaying plant specimens in the manner of a botanical Garden.

As more exotic specimens were introduced, a conservatory was constructed to house tropical plants such as sugar cane, coffee, tea, ginger and cotton as well as orchids and epiphytes. A pond was formed to contain a large rare water-lily, the Victoria amazonica.

Although the pond and the conservatory have now gone, the ten-acre gardens are still a listed Botanical Garden and contain many varieties of trees, deciduous and evergreen, native and exotic. These include: lime; yew; holly; oak; beech; elm; common pear tree; silver birch; and walnut trees. Rarer varieties include: cut-leaved alder; three cut-leaved hornbeams; red horse chestnut; monkey puzzle (Araucaria); and Indian chestnut.