Restoration is becoming a quite complex process: a large number of internal and external variables co-exist and may impair it. Among these, the large number of professionals involved and the huge amount of documentation produced can heavily affect the quality of the intervention as well as the possibility to have systemic and informed interventions in the future. In particular, a standardized method for storing restoration data and accessing them is still lacking, and the use of new technologies is still limited and/or not scalable. The paper describes the process of designing and testing an information system (IS) based on three-dimensional (3D) data, aimed to support the restoration of Neptune's Fountain in Bologna. In preparation of the restoration, a major effort was carried out to design and implement a web-based IS able to host all of the data produced, to allow the conservation-restoration specialists to interact on-site with an accurate 3D representation of the elements of the fountain, and to directly reference all information and data produced on the geometry of the model. The paper focuses on the challenges and adopted solutions related to the use of 3D models and the data mapping on 3D surfaces in the context of restoration documentation. Highly detailed visualizations of the models, easy navigation, and usable functionalities to add information directly on the 3D model have been achieved by extending the available solutions and by implementing new mechanisms to overcome the limitations of WebGL and remote rendering. Neptune IS’ development has been extensively experimented in a real context of use. Results and knowledge from the experimentation currently represents the basis for evolving Neptune IS into a possible generic and flexible platform for documentation management in the field of restoration and related methodologies.