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Over centuries, hundreds of thousands of historical sources that contain information on the Viennese Danube river landscape have been stored in various archives. This unique wealth of historical material provides an excellent basis for the in-depth GIS reconstruction of Vienna’s topography over the past 500 years. However, the numerous – partly contradictory – sources must be critically assessed, making an authoritative reconstruction even more complicated. This paper describes the different types of historical sources used for the GIS-based reconstruction, the underlying methodological approach and its limitations regarding reliability and information value. The reconstruction was based on three cornerstones: (1) the available historical sources; (2) knowledge about morphological processes typical for the Austrian Danube prior to regulation; and (3) the interpretation of past hydraulic measures with respect to their effectiveness and their impact on the river’s behaviour. The current state of the Viennese river landscape served as a starting point for the GIS work; from there, ten historical states were reconstructed step-by-step going backwards in time to the least well-known situation in the early 16th century. After one reconstruction had been completed, its relevance for the temporally younger situations was evaluated. Such a regressive-iterative approach allows for permanent critical revision of the reconstructed time segments already processed. The resulting maps of the Danube floodplain from 1529 to 2010 provide a solid basis for interpreting the environmental conditions for Vienna’s urban development. They also help to localise certain riverine and urban landmarks (such as river arms or bridges) relevant for the history of Vienna. We conclude that the diversity of approaches and findings of the historical and natural sciences (river morphology, hydrology) provide key synergies.