Archaeological research relies on the documentation and analysis of archaeological entities in space and time, i.e. the stratigraphic ordering of these units, resulting in a stratigraphic sequence. A GIS-based Archaeological Information System (AIS) organises archaeological entities and associated attributable information according to its specific three-dimensional geographical position based on the framework provided by a Geographical Information System (GIS). To compile a stratigraphic sequence of these entities located in space, the GIS-based AIS must be extended by a fourth dimension – time. The paper presents the associated extension of ArcGIS (ESRI) by a stratigraphic sequence composer with an integrated interval-based time model as the basic digital environment for spatio-temporal analysis of archaeological excavation datasets. The long-term excavation at Tell el-Daba, Egypt was chosen as a case study to evaluate the applicability of various digital analysis tools using a geo-referenced 4D AIS on non-digital and incomplete excavation datasets. As most existing archaeological excavation datasets are based upon long-term inconsistent and analogue data, it is crucial to integrate and handle such data to ensure their accessibility for state-of-the-art archaeological spatio-temporal data analysis.