Highlights: A virtual 3D model of a botanical garden was built based on a GIS with plants botanical information and buildings, statues and other assets historical information. The height and crown diameter of individual trees were determined from watershed operations on aerial LiDAR data. Statues were modelled photogrammetrically. Buildings were modelled procedurally using CGA rules. Users found realism and information access to be the most positive points. The way of data organisation and the elaborated modelling rules make the product easily extendable for new data and objects. Abstract: Botanical gardens are important spots in urban spaces, both for researchers and for many different kinds of public. Conveying scientific information by means of an attractive digital product, on a pre- or post-visit experience, is a way of captivating the public, especially the younger generation, to the relevance of those gardens as repositories of knowledge and for conservation of plant species diversity. This approach also facilitates communication with the general public and access to historical data. On the other hand, bringing the garden to the desktop of researchers and managers can be an advantage, not only for an overview of the status quo but also in spatial planning matters. This paper describes the production of a 3D dynamic model of the Tropical Botanical Garden in Lisbon on top of a Geographic Information System (GIS). Its development included creating a spatial database to organise data originating from a variety of sources, the three-dimensional (3D) modelling of plants, buildings and statues, the creation of web pages with historic and contextual information, as well as the publication of a number of interactive 3D scenes. Several software packages were used, and the final outputs were published in ArcGIS Online to be explored by the public and researchers (link provided at the end of the text). The data are organised in a database, and most 3D modelling tasks are procedural through Computer Generated Architecture (CGA) rules. Thus, updating information or 3D models can be done without having to repeat all steps, an important feature for a dynamic botanical garden. Challenges and solutions are also addressed, providing a constructive contribution to the further implementation of similar experiences in other botanical gardens. According to a user survey carried out, the realism of the representation and the possibility of easily retrieving information from the objects are the most positive aspects of the project.