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River/floodplain restoration programs are often based on type-specific reference conditions of the respective river section. Most large rivers in the industrialized world are heavily degraded and lack near-natural reference sites. For that reason, historical analyses of the pre-channelization state have been used to define adequate restoration targets at the Austrian Danube section in the Alluvial Zone National Park downstream from Vienna. This study compares new reference data derived from 3D-reconstructions in the form of digital terrain models from two historical Danube river landscapes: the Machland floodplain in 1812 and the former floodplain in Vienna in 1849. The focus is on the original hydrological surface and subsurface connectivity of the river-floodplain systems related to different flow situations. Here, we use water cover, shorelines, depth of the groundwater table and inundation depth as surrogates for measuring connectivity. The results show that the two study sites naturally constituted extreme formations of the Austrian anabranching Danube sections. The Machland section was one of the narrowest floodplains but highly dynamic, and the Vienna/Lobau section was one of the broadest, whereby only the central part close to the main channel originally showed high morphological turnover. The analyses of hydrological surface connectivity relative to total floodplain extension reveal significant differences due to their basic geological and geographical conditions. Despite these basic differences, both study sites - in absolute numbers - showed similar extensions of the water bodies at low and mean flow. The depths of the groundwater table related to mean flow were also comparable. Prior to channelization, the groundwater conditions in both floodplains favored the formation of wet to moist alluvial forest communities. Up until today, the two river landscapes continue to undergo different developments: both river sections are impounded, but the Machland floodplain still represents a rural site while the Vienna site has been utilized more intensively as building land and for urban infrastructure. As a consequence of the diverse human interventions in the 19th and 20th century, river bed degradation and aggradation of sediments in the floodplains have significantly truncated fluvial dynamics and hydrological connectivity. In addition, these phenomena have substantially deepened the groundwater table in both study sites. The results contribute to the identification of river/floodplain-type-specific reference conditions and provide an additional decision basis for discussing appropriate management strategies in the degraded riverine ecosystems.