Advanced analysis of spatio-temporal data is improving our knowledge about natural phenomena such as landslides and volcanic activity. Furthermore, it can contribute to a deeper understanding of the built environment by predicting city development. However, the data produced by the modelling of these observations can easily rise to terra bytes of 4D (3D space plus time) data. Also, the repeatability of such analysis is essential. Thus, repeatable and reliable access to big spatio-temporal data, models and simulation results should be guaranteed. However, today´s Geographic Information Systems (GIS) are not prepared to meet these requirements. Therefore, we present a comprehensive spatio-temporal data model for GIS and geodatabase management systems that can be used as the “heart” of 4D GIS. The comprehensive model enables a flexible management of time- series-based geometric and topological data. It cares of storage reduction and computational efficiency when storing, retrieving, and processing surface- and volume-based data in 3D space plus time. Furthermore, the model can handle geometry and topology changes of 4D data, i.e., mesh changes of triangulated surfaces and tetrahedral volumes over time. The model also allows the attachment of detailed semantic information to geometric and topological entities. The various concepts, implementation and the benefits of our comprehensive model are presented. Finally, conclusions are drawn from the approach and an outlook is given on future research including demanding applications based on multi-scale digital elevation models.